İsmail İlkan Ceylan

Xingyue Huang, Miguel Romero Orth, İsmail İlkan Ceylan et al.

Graph neural networks are prominent models for representation learning over graph-structured data. While the capabilities and limitations of these models are well-understood for simple graphs, our understanding remains incomplete in the context of knowledge graphs. Our goal is to provide a systematic understanding of the landscape of graph neural networks for knowledge graphs pertaining to the prominent task of link prediction. Our analysis entails a unifying perspective on seemingly unrelated models and unlocks a series of other models. The expressive power of various models is characterized via a corresponding relational Weisfeiler-Leman algorithm. This analysis is extended to provide a precise logical characterization of the class of functions captured by a class of graph neural networks. The theoretical findings presented in this paper explain the benefits of some widely employed practical design choices, which are validated empirically.

Ben Finkelshtein, Xingyue Huang, Michael Bronstein et al.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

Ralph Abboud, Radoslav Dimitrov, İsmail İlkan Ceylan

Most graph neural network models rely on a particular message passing paradigm, where the idea is to iteratively propagate node representations of a graph to each node in the direct neighborhood. While very prominent, this paradigm leads to information propagation bottlenecks, as information is repeatedly compressed at intermediary node representations, which causes loss of information, making it practically impossible to gather meaningful signals from distant nodes. To address this, we propose shortest path message passing neural networks, where the node representations of a graph are propagated to each node in the shortest path neighborhoods. In this setting, nodes can directly communicate between each other even if they are not neighbors, breaking the information bottleneck and hence leading to more adequately learned representations. Our framework generalizes message passing neural networks, resulting in a class of more expressive models, including some recent state-of-the-art models. We verify the capacity of a basic model of this framework on dedicated synthetic experiments, and on real-world graph classification and regression benchmarks, and obtain state-of-the art results.

Sam Adam-Day, Theodor Mihai Iliant, İsmail İlkan Ceylan

Graph neural networks (GNNs) are the de facto standard deep learning architectures for machine learning on graphs. This has led to a large body of work analyzing the capabilities and limitations of these models, particularly pertaining to their representation and extrapolation capacity. We offer a novel theoretical perspective on the representation and extrapolation capacity of GNNs, by answering the question: how do GNNs behave as the number of graph nodes become very large? Under mild assumptions, we show that when we draw graphs of increasing size from the Erdős-Rényi model, the probability that such graphs are mapped to a particular output by a class of GNN classifiers tends to either zero or to one. This class includes the popular graph convolutional network architecture. The result establishes 'zero-one laws' for these GNNs, and analogously to other convergence laws, entails theoretical limitations on their capacity. We empirically verify our results, observing that the theoretical asymptotic limits are evident already on relatively small graphs.

Krzysztof Olejniczak, Radoslav Dimitrov, Xingyue Huang et al.

Formal theorem provers based on large language models (LLMs) are highly sensitive to superficial variations in problem representation: semantically equivalent statements can exhibit drastically different proof success rates, revealing a failure to respect structural symmetries inherent in formal mathematics. This raises a central question: what are the right symmetries for formal theorem proving? We introduce rewriting categories, a category-theoretic framework capturing the compositional, generally non-invertible transformations induced by proof tactics, and use it to formalize two symmetry notions: proof equivariance, governing how proof distributions transform under rewrites, and success invariance (i.e., invariance of success probability), requiring equivalent statements to be solved with the same probability. We observe that state-based next-tactic provers naturally satisfy proof equivariance by operating on proof states. In contrast, state-of-the-art LLM-based provers satisfy neither property, exhibiting large performance variation across equivalent formulations. To mitigate this, we propose test-time methods that aggregate over equivalent rewritings of the input, showing theoretically that they recover success invariance in the sampling limit, and empirically, that they improve robustness and performance under fixed inference budgets. Our results highlight symmetry as a key missing inductive bias in LLM-based theorem proving and suggest test-time computation as a practical route to approximate it.

Radoslav Dimitrov, Zeyang Zhao, Ralph Abboud et al.

Graph neural networks are prominent models for representation learning over graphs, where the idea is to iteratively compute representations of nodes of an input graph through a series of transformations in such a way that the learned graph function is isomorphism invariant on graphs, which makes the learned representations graph invariants. On the other hand, it is well-known that graph invariants learned by these class of models are incomplete: there are pairs of non-isomorphic graphs which cannot be distinguished by standard graph neural networks. This is unsurprising given the computational difficulty of graph isomorphism testing on general graphs, but the situation begs to differ for special graph classes, for which efficient graph isomorphism testing algorithms are known, such as planar graphs. The goal of this work is to design architectures for efficiently learning complete invariants of planar graphs. Inspired by the classical planar graph isomorphism algorithm of Hopcroft and Tarjan, we propose PlanE as a framework for planar representation learning. PlanE includes architectures which can learn complete invariants over planar graphs while remaining practically scalable. We empirically validate the strong performance of the resulting model architectures on well-known planar graph benchmarks, achieving multiple state-of-the-art results.

Krzysztof Olejniczak, Xingyue Huang, Mikhail Galkin et al.

Motivated by the incompleteness of modern knowledge graphs, a new setup for query answering has emerged, where the goal is to predict answers that do not necessarily appear in the knowledge graph, but are present in its completion. In this paper, we formally introduce and study two query answering problems, namely, query answer classification and query answer retrieval. To solve these problems, we propose AnyCQ, a model that can classify answers to any conjunctive query on any knowledge graph. At the core of our framework lies a graph neural network trained using a reinforcement learning objective to answer Boolean queries. Trained only on simple, small instances, AnyCQ generalizes to large queries of arbitrary structure, reliably classifying and retrieving answers to queries that existing approaches fail to handle. This is empirically validated through our newly proposed, challenging benchmarks. Finally, we empirically show that AnyCQ can effectively transfer to completely novel knowledge graphs when equipped with an appropriate link prediction model, highlighting its potential for querying incomplete data.

Xingyue Huang, Louis Tichelman, Jinwoo Kim et al.

Relational learning is a challenging problem that has motivated a wide range of approaches, including graph-based models (e.g., graph neural networks, graph transformers), tabular methods (e.g., tabular foundation models), and sequence-based approaches (e.g., large language models), each with its own advantages and limitations. We propose RelAgent, an LLM-based autonomous data scientist for relational learning, which operates in two phases. In the search phase, an LLM agent uses database, validation, and evaluation workspace tools to construct SQL feature programs and select a predictive model. In the inference phase, the resulting program is executed without further LLM calls. The final predictor consists of SQL queries and a classical model, enabling fast, deterministic, and intrinsically interpretable predictions: features are human-readable queries, and predictions depend only on the resulting query-defined feature map, enabling scalable deployment using standard database systems.

Péter Mernyei, Konstantinos Meichanetzidis, İsmail İlkan Ceylan

We investigate quantum circuits for graph representation learning, and propose equivariant quantum graph circuits (EQGCs), as a class of parameterized quantum circuits with strong relational inductive bias for learning over graph-structured data. Conceptually, EQGCs serve as a unifying framework for quantum graph representation learning, allowing us to define several interesting subclasses which subsume existing proposals. In terms of the representation power, we prove that the studied subclasses of EQGCs are universal approximators for functions over the bounded graph domain. This theoretical perspective on quantum graph machine learning methods opens many directions for further work, and could lead to models with capabilities beyond those of classical approaches. We empirically verify the expressive power of EQGCs through a dedicated experiment on synthetic data, and additionally observe that the performance of EQGCs scales well with the depth of the model and does not suffer from barren plateu issues.

Johannes Messner, Ralph Abboud, İsmail İlkan Ceylan

Knowledge graph completion is the task of inferring missing facts based on existing data in a knowledge graph. Temporal knowledge graph completion (TKGC) is an extension of this task to temporal knowledge graphs, where each fact is additionally associated with a time stamp. Current approaches for TKGC primarily build on existing embedding models which are developed for (static) knowledge graph completion, and extend these models to incorporate time, where the idea is to learn latent representations for entities, relations, and timestamps and then use the learned representations to predict missing facts at various time steps. In this paper, we propose BoxTE, a box embedding model for TKGC, building on the static knowledge graph embedding model BoxE. We show that BoxTE is fully expressive, and possesses strong inductive capacity in the temporal setting. We then empirically evaluate our model and show that it achieves state-of-the-art results on several TKGC benchmarks.

Ralph Abboud, İsmail İlkan Ceylan

Node classification and link prediction are widely studied in graph representation learning. While both transductive node classification and link prediction operate over a single input graph, they have so far been studied separately. Node classification models take an input graph with node features and incomplete node labels, and implicitly assume that the graph is relationally complete, i.e., no edges are missing. By contrast, link prediction models are solely motivated by relational incompleteness of the input graphs, and do not typically leverage node features or classes. We propose a unifying perspective and study the problems of (i) transductive node classification over incomplete graphs and (ii) link prediction over graphs with node features, introduce a new dataset for this setting, WikiAlumni, and conduct an extensive benchmarking study.

Ralph Abboud, İsmail İlkan Ceylan, Martin Grohe et al.

Graph neural networks (GNNs) are effective models for representation learning on relational data. However, standard GNNs are limited in their expressive power, as they cannot distinguish graphs beyond the capability of the Weisfeiler-Leman graph isomorphism heuristic. In order to break this expressiveness barrier, GNNs have been enhanced with random node initialization (RNI), where the idea is to train and run the models with randomized initial node features. In this work, we analyze the expressive power of GNNs with RNI, and prove that these models are universal, a first such result for GNNs not relying on computationally demanding higher-order properties. This universality result holds even with partially randomized initial node features, and preserves the invariance properties of GNNs in expectation. We then empirically analyze the effect of RNI on GNNs, based on carefully constructed datasets. Our empirical findings support the superior performance of GNNs with RNI over standard GNNs.

Ralph Abboud, İsmail İlkan Ceylan, Thomas Lukasiewicz et al.

Knowledge base completion (KBC) aims to automatically infer missing facts by exploiting information already present in a knowledge base (KB). A promising approach for KBC is to embed knowledge into latent spaces and make predictions from learned embeddings. However, existing embedding models are subject to at least one of the following limitations: (1) theoretical inexpressivity, (2) lack of support for prominent inference patterns (e.g., hierarchies), (3) lack of support for KBC over higher-arity relations, and (4) lack of support for incorporating logical rules. Here, we propose a spatio-translational embedding model, called BoxE, that simultaneously addresses all these limitations. BoxE embeds entities as points, and relations as a set of hyper-rectangles (or boxes), which spatially characterize basic logical properties. This seemingly simple abstraction yields a fully expressive model offering a natural encoding for many desired logical properties. BoxE can both capture and inject rules from rich classes of rule languages, going well beyond individual inference patterns. By design, BoxE naturally applies to higher-arity KBs. We conduct a detailed experimental analysis, and show that BoxE achieves state-of-the-art performance, both on benchmark knowledge graphs and on more general KBs, and we empirically show the power of integrating logical rules.

Ralph Abboud, İsmail İlkan Ceylan, Radoslav Dimitrov

Weighted model counting (WMC) consists of computing the weighted sum of all satisfying assignments of a propositional formula. WMC is well-known to be #P-hard for exact solving, but admits a fully polynomial randomized approximation scheme (FPRAS) when restricted to DNF structures. In this work, we study weighted model integration, a generalization of weighted model counting which involves real variables in addition to propositional variables, and pose the following question: Does weighted model integration on DNF structures admit an FPRAS? Building on classical results from approximate volume computation and approximate weighted model counting, we show that weighted model integration on DNF structures can indeed be approximated for a class of weight functions. Our approximation algorithm is based on three subroutines, each of which can be a weak (i.e., approximate), or a strong (i.e., exact) oracle, and in all cases, comes along with accuracy guarantees. We experimentally verify our approach over randomly generated DNF instances of varying sizes, and show that our algorithm scales to large problem instances, involving up to 1K variables, which are currently out of reach for existing, general-purpose weighted model integration solvers.

İsmail İlkan Ceylan, Rafael Peñaloza

Many formalisms combining ontology languages with uncertainty, usually in the form of probabilities, have been studied over the years. Most of these formalisms, however, assume that the probabilistic structure of the knowledge remains static over time. We present a general approach for extending ontology languages to handle time-evolving uncertainty represented by a dynamic Bayesian network. We show how reasoning in the original language and dynamic Bayesian inferences can be exploited for effective reasoning in our framework.

Diego Calvanese, İsmail İlkan Ceylan, Marco Montali et al.

Knowledge and Action Bases (KABs) have been recently proposed as a formal framework to capture the dynamics of systems which manipulate Description Logic (DL) Knowledge Bases (KBs) through action execution. In this work, we enrich the KAB setting with contextual information, making use of different context dimensions. On the one hand, context is determined by the environment using context-changing actions that make use of the current state of the KB and the current context. On the other hand, it affects the set of TBox assertions that are relevant at each time point, and that have to be considered when processing queries posed over the KAB. Here we extend to our enriched setting the results on verification of rich temporal properties expressed in mu-calculus, which had been established for standard KABs. Specifically, we show that under a run-boundedness condition, verification stays decidable.