arXiv subjects

Martin Grohe

Publications and source records attributed to Martin Grohe.

At least 19 recordsLinked to original sources

arXiv2026

First-Order Query Evaluation with Cardinality Conditions

We study an extension of first-order logic that allows to express cardinality conditions in a similar way as SQL's COUNT operator. The corresponding logic FOC(P) was introduced by Kuske and Schweikardt (LICS 2017), who showed that query evaluation for this logic is fixed-parameter tractable on classes of databases of bounded degree. In the present paper, we first show that the fixed-parameter tractability of FOC(P) cannot even be generalised to very simple classes of databases of unbounded degree, such as unranked trees or strings with a linear order relation. Then we identify a fragment FOC_1(P) of FOC(P) which is still sufficiently strong to express standard applications of SQL's COUNT operator. Our main result shows that query evaluation for FOC_1(P) is fixed-parameter tractable on nowhere-dense classes of databases.

cs.LO↗

arXiv2026

A Rank-Preserving Gaifman Normal Form

We introduce a rank measure for first-order logic and prove a "rank-preserving'" version of Gaifman's theorem. Compared to earlier "rank-preserving locality theorems'" (in particular, [Grohe, Kreutzer, Siebertz, JACM 2017]), our theorem is not only much simpler, but also yields formulas in exactly the same normal form as Gaifman's original theorem. As an application of this theorem, we give a simplified proof of the main result of [Grohe, Kreutzer, Siebertz, JACM 2017] that first-order properties of nowhere-dense structures can be decided in almost linear time.

cs.LO↗

arXiv2026

Amortized Molecular Optimization via Group Relative Policy Optimization

In structurally constrained molecular optimization, state-of-the-art methods restart an expensive oracle-driven search from scratch for every new input structure, scaling poorly to settings with many starting structures or expensive oracles. While amortized approaches that learn a transferable policy could in principle remove this bottleneck, existing methods struggle to generalize to diverse structural constraints at inference time. We present AMORTIX, an amortized Graph Transformer model that natively supports such constraints, optimizing molecular structures in a single forward pass with zero inference-time oracle calls. A central challenge for amortized training in this domain is that optimization difficulty varies drastically across starting structures. We show that, under this heterogeneity, standard reinforcement learning methods fail to stabilize training, and address this by normalizing rewards within groups of completions sharing the same starting structure. We evaluate on structurally constrained single- and multi-target kinase inhibitor design, and on a few-shot prodrug case study. AMORTIX outperforms both amortized and instance-optimization baselines on goal-directed scaffold decoration and ranks first among amortized methods on the PMO benchmark; the prodrug case study further demonstrates transfer of a learned modification rule to unseen drug structures. Code is available at https://github.com/Hash-hh/AMORTIX/.

cs.LG↗

arXiv2026

Tabular foundation models for in-context prediction of molecular properties

Accurate molecular property prediction is central to drug discovery, catalysis, and process design, yet real-world applications are often limited by small datasets. Molecular foundation models provide a promising direction by learning transferable molecular representations; however, they typically involve task-specific fine-tuning, require machine learning expertise, and often fail to outperform classical baselines. Tabular foundation models (TFMs) offer a fundamentally different paradigm: they perform predictions through in-context learning, enabling inference without task-specific training. Here, we evaluate TFMs in the low- to medium-data regime across both standardized pharmaceutical benchmarks and chemical engineering datasets. We evaluate both frozen molecular foundation model representations, as well as classical descriptors and fingerprints. Across the benchmarks, the approach shows excellent predictive performance while reducing computational cost, compared to fine-tuning, with these advantages also transferring to practical engineering data settings. In particular, combining TFMs with CheMeleon embeddings yields up to 100\% win rates on 30 MoleculeACE tasks, while compact RDKit2d and Mordred descriptors provide strong descriptor-based alternatives. Molecular representation emerges as a key determinant in TFM performance, with molecular foundation model embeddings and 2D descriptor sets both providing substantial gains over classic molecular fingerprints on many tasks. These results suggest that in-context learning with TFMs provides a highly accurate and cost-efficient alternative for property prediction in practical applications.

cs.LG↗

arXiv2026

Robust Graph Isomorphism, Quadratic Assignment and VC Dimension

We present an additive $\varepsilon n^{2}$-approximation algorithm for the Graph Edit Distance problem (GED) on graphs of VC dimension $d$ running in time $n^{O(d/\varepsilon^{2})}$. In particular, this recovers a previous result by Arora, Frieze, and Kaplan [Math. Program. 2002] who gave an $\varepsilon n^{2}$-approximation running in time $n^{O(\log n/\varepsilon^{2})}$. Similar to the work of Arora et al., we extend our results to arbitrary Quadratic Assignment problems (QAPs) by introducing a notion of VC dimension for QAP instances, and giving an $\varepsilon n^{2}$-approximation for QAPs with bounded weights running in time $n^{O(\varepsilon^{-2}(d + \log\varepsilon^{-1}))}$. As a particularly interesting special case, we further study the problem $\varepsilon$-$\mathsf{GI}$, which entails determining if two graphs $G,H$ over $n$ vertices are isomorphic, when promised that if they are not, their graph edit distance is at least $\varepsilon n^{2}$. We show that the standard Weisfeiler--Leman algorithm of dimension $O(\varepsilon^{-1}d\log(\varepsilon^{-1}))$ solves this problem on graphs of VC dimension $d$. We also show that dimension $O(\varepsilon^{-1}\log n)$ suffices on arbitrary $n$-vertex graphs, while $k$-WL fails on instances at distance $Ω(n^{2}/k)$.

cs.DS↗

arXiv2026

Isomorphism for Tournaments of Small Twin Width

We prove that isomorphism of tournaments of twin width at most $k$ can be decided in time $k^{O(\log k)}n^{O(1)}$. This implies that the isomorphism problem for classes of tournaments of bounded or moderately growing twin width is in polynomial time. By comparison, there are classes of undirected graphs of bounded twin width that are isomorphism complete, that is, the isomorphism problem for the classes is as hard as the general graph isomorphism problem. Twin width is a graph parameter that has been introduced only recently (Bonnet et al., J. ACM 2022), but has received a lot of attention in structural graph theory since then. On directed graphs, it is functionally smaller than clique width. We prove that on tournaments (but not on general directed graphs) it is also functionally smaller than directed tree width (and thus, the same also holds for cut width and directed path width). Hence, our result implies that tournament isomorphism testing is also fixed-parameter tractable when parameterized by any of these parameters. Our isomorphism algorithm heavily employs group-theoretic techniques. This seems to be necessary: as a second main result, we show that the combinatorial Weisfeiler-Leman algorithm does not decide isomorphism of tournaments of twin width at most 35 if its dimension is $o(n)$. (Throughout this abstract, $n$ is the order of the input graphs.)

cs.DS↗

arXiv2026

The Complexity of Homomorphism Reconstruction Revisited

We revisit the algorithmic problem of reconstructing a graph from homomorphism counts that has first been studied in (Böker et al., STACS 2024): given graphs $F_1,\ldots,F_k$ and counts $m_1,\ldots,m_k$, decide if there is a graph $G$ such that the number of homomorphisms from $F_i$ to $G$ is $m_i$, for all $i$. We prove that the problem is NEXP-hard if the counts $m_i$ are specified in binary and $Σ_2^p$-complete if they are in unary. Furthermore, as a positive result, we show that the unary version can be solved in polynomial time if the constraint graphs are stars of bounded size.

cs.DM↗

arXiv2026

How Expressive Are Graph Neural Networks in the Presence of Node Identifiers?

Graph neural networks (GNNs) are a widely used class of machine learning models for graph-structured data, based on local aggregation over neighbors. GNNs have close connections to logic. In particular, their expressive power is linked to that of modal logics and bounded-variable logics with counting. In many practical scenarios, graphs processed by GNNs have node features that act as unique identifiers. In this work, we study how such identifiers affect the expressive power of GNNs. We initiate a study of the key-invariant expressive power of GNNs, inspired by the notion of order-invariant definability in finite model theory: which node queries that depend only on the underlying graph structure can GNNs express on graphs with unique node identifiers? We provide answers for various classes of GNNs with local max- or sum-aggregation.

cs.LO↗

arXiv2026

Query Languages for Machine-Learning Models

In this paper, I discuss two logics for weighted finite structures: first-order logic with summation (FO(SUM)) and its recursive extension IFP(SUM). These logics originate from foundational work by Grädel, Gurevich, and Meer in the 1990s. In recent joint work with Standke, Steegmans, and Van den Bussche, we have investigated these logics as query languages for machine learning models, specifically neural networks, which are naturally represented as weighted graphs. I present illustrative examples of queries to neural networks that can be expressed in these logics and discuss fundamental results on their expressiveness and computational complexity.

cs.LO↗

arXiv2026

Recursive querying of neural networks via weighted structures

Expressive querying of machine learning models - viewed as a form of intentional data - enables their verification and interpretation using declarative languages, thereby making learned representations of data more accessible. Motivated by the querying of feedforward neural networks, we investigate logics for weighted structures. In the absence of a bound on neural network depth, such logics must incorporate recursion; thereto we revisit the functional fixpoint mechanism proposed by Grädel and Gurevich. We adopt it in a Datalog-like syntax; we extend normal forms for fixpoint logics to weighted structures; and show an equivalent "loose" fixpoint mechanism that allows values of inductively defined weight functions to be overwritten. We propose a "scalar" restriction of functional fixpoint logic, of polynomial-time data complexity, and show it can express all PTIME model-agnostic queries over reduced networks with polynomially bounded weights. In contrast, we show that very simple model-agnostic queries are already NP-complete. Finally, we consider transformations of weighted structures by iterated transductions.

cs.LO↗

arXiv2025

Repetition Makes Perfect: Recurrent Graph Neural Networks Match Message-Passing Limit

We precisely characterize the expressivity of computable Recurrent Graph Neural Networks (recurrent GNNs). We prove that recurrent GNNs with finite-precision parameters, sum aggregation, and ReLU activation, can compute any graph algorithm that respects the natural message-passing invariance induced by the Color Refinement (or Weisfeiler-Leman) algorithm. While it is well known that the expressive power of GNNs is limited by this invariance [Morris et al., AAAI 2019; Xu et al., ICLR 2019], we establish that recurrent GNNs can actually match this limit. This is in contrast to non-recurrent GNNs, which have the power of Weisfeiler-Leman only in a very weak, "non-uniform", sense where each graph size requires a different GNN to compute with. Our construction introduces only a polynomial overhead in both time and space. Furthermore, we show that by incorporating random initialization, for connected graphs recurrent GNNs can express all graph algorithms. In particular, any polynomial-time graph algorithm can be emulated on connected graphs in polynomial time by a recurrent GNN with random initialization.

cs.LG↗

arXiv2025

Automorphism groups of graphs of bounded Hadwiger number

We determine the structure of automorphism groups of finite graphs of bounded Hadwiger number. Our proof includes a structural analysis of finite edge-transitive graphs. In particular, we show that for connected, $K_{h+1}$-minor-free, edge-transitive, twin-free, finite graphs the non-abelian composition factors of the automorphism group have bounded order. We use this to show that the automorphism groups of finite graphs of bounded Hadwiger number are obtained by repeated group extensions using abelian groups, symmetric groups and groups of bounded order.

math.CO↗

arXiv2025

Molecular Machine Learning in Chemical Process Design

We present a perspective on molecular machine learning (ML) in the field of chemical process engineering. Recently, molecular ML has demonstrated great potential in (i) providing highly accurate predictions for properties of pure components and their mixtures, and (ii) exploring the chemical space for new molecular structures. We review current state-of-the-art molecular ML models and discuss research directions that promise further advancements. This includes ML methods, such as graph neural networks and transformers, which can be further advanced through the incorporation of physicochemical knowledge in a hybrid or physics-informed fashion. Then, we consider leveraging molecular ML at the chemical process scale, which is highly desirable yet rather unexplored. We discuss how molecular ML can be integrated into process design and optimization formulations, promising to accelerate the identification of novel molecules and processes. To this end, it will be essential to create molecule and process design benchmarks and practically validate proposed candidates, possibly in collaboration with the chemical industry.

physics.chem-ph↗

arXiv2025

Learning from Algorithm Feedback: One-Shot SAT Solver Guidance with GNNs

Boolean Satisfiability (SAT) solvers are foundational to computer science, yet their performance typically hinges on hand-crafted heuristics. This work introduces Reinforcement Learning from Algorithm Feedback (RLAF) as a paradigm for learning to guide SAT solver branching heuristics with Graph Neural Networks (GNNs). Central to our approach is a novel and generic mechanism for injecting inferred variable weights and polarities into the branching heuristics of existing SAT solvers. In a single forward pass, a GNN assigns these parameters to all variables. Casting this one-shot guidance as a reinforcement learning problem lets us train the GNN with off-the-shelf policy-gradient methods, such as GRPO, directly using the solver's computational cost as the sole reward signal. Extensive evaluations demonstrate that RLAF-trained policies significantly reduce the mean solve times of different base solvers across diverse SAT problem distributions, achieving more than a 2x speedup in some cases, while generalizing effectively to larger and harder problems after training. Notably, these policies consistently outperform expert-supervised approaches based on learning handcrafted weighting heuristics, offering a promising path towards data-driven heuristic design in combinatorial optimization.

cs.LG↗

arXiv2025

GraphXForm: Graph transformer for computer-aided molecular design

Generative deep learning has become pivotal in molecular design for drug discovery, materials science, and chemical engineering. A widely used paradigm is to pretrain neural networks on string representations of molecules and fine-tune them using reinforcement learning on specific objectives. However, string-based models face challenges in ensuring chemical validity and enforcing structural constraints like the presence of specific substructures. We propose to instead combine graph-based molecular representations, which can naturally ensure chemical validity, with transformer architectures, which are highly expressive and capable of modeling long-range dependencies between atoms. Our approach iteratively modifies a molecular graph by adding atoms and bonds, which ensures chemical validity and facilitates the incorporation of structural constraints. We present GraphXForm, a decoder-only graph transformer architecture, which is pretrained on existing compounds and then fine-tuned using a new training algorithm that combines elements of the deep cross-entropy method and self-improvement learning. We evaluate GraphXForm on various drug design tasks, demonstrating superior objective scores compared to state-of-the-art molecular design approaches. Furthermore, we apply GraphXForm to two solvent design tasks for liquid-liquid extraction, again outperforming alternative methods while flexibly enforcing structural constraints or initiating design from existing molecular structures.

cs.LG↗

arXiv2025

Some Thoughts on Graph Similarity

We give an overview of different approaches to measuring the similarity of, or the distance between, two graphs, highlighting connections between these approaches. We also discuss the complexity of computing the distances.

cs.DM↗

arXiv2025

Homomorphism Tensors and Linear Equations

Lovász (1967) showed that two graphs $G$ and $H$ are isomorphic if and only if they are homomorphism indistinguishable over the class of all graphs, i.e. for every graph $F$, the number of homomorphisms from $F$ to $G$ equals the number of homomorphisms from $F$ to $H$. Recently, homomorphism indistinguishability over restricted classes of graphs such as bounded treewidth, bounded treedepth and planar graphs, has emerged as a surprisingly powerful framework for capturing diverse equivalence relations on graphs arising from logical equivalence and algebraic equation systems. In this paper, we provide a unified algebraic framework for such results by examining the linear-algebraic and representation-theoretic structure of tensors counting homomorphisms from labelled graphs. The existence of certain linear transformations between such homomorphism tensor subspaces can be interpreted both as homomorphism indistinguishability over a graph class and as feasibility of an equational system. Following this framework, we obtain characterisations of homomorphism indistinguishability over several natural graph classes, namely trees of bounded degree and graphs of bounded pathwidth, answering a question of Dell et al. (2018), and graphs of bounded treedepth.

math.CO↗

arXiv2025

Compressing CFI Graphs and Lower Bounds for the Weisfeiler-Leman Refinements

The $k$-dimensional Weisfeiler-Leman ($k$-WL) algorithm is a simple combinatorial algorithm that was originally designed as a graph isomorphism heuristic. It naturally finds applications in Babai's quasipolynomial time isomorphism algorithm, practical isomorphism solvers, and algebraic graph theory. However, it also has surprising connections to other areas such as logic, proof complexity, combinatorial optimization, and machine learning. The algorithm iteratively computes a coloring of the $k$-tuples of vertices of a graph. Since Fürer's linear lower bound [ICALP 2001], it has been an open question whether there is a super-linear lower bound for the iteration number for $k$-WL on graphs. We answer this question affirmatively, establishing an $Ω(n^{k/2})$-lower bound for all $k$.

cs.DM↗