arXiv subjects

Martin Grohe

Publications and source records attributed to Martin Grohe.

At least 19 recordsLinked to original sources

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

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 $\Omega(n^{2}/k)$.

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 (B\"oker 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 $\Sigma_2^p$-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

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

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 Gr\"adel, 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 Gr\"adel 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

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

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↗

arXiv2024

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↗

arXiv2024

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↗

arXiv2024

Query languages for neural networks

We lay the foundations for a database-inspired approach to interpreting and understanding neural network models by querying them using declarative languages. Towards this end we study different query languages, based on first-order logic, that mainly differ in their access to the neural network model. First-order logic over the reals naturally yields a language which views the network as a black box; only the input--output function defined by the network can be queried. This is essentially the approach of constraint query languages. On the other hand, a white-box language can be obtained by viewing the network as a weighted graph, and extending first-order logic with summation over weight terms. The latter approach is essentially an abstraction of SQL. In general, the two approaches are incomparable in expressive power, as we will show. Under natural circumstances, however, the white-box approach can subsume the black-box approach; this is our main result. We prove the result concretely for linear constraint queries over real functions definable by feedforward neural networks with a fixed number of hidden layers and piecewise linear activation functions.

cs.AI↗

arXiv2024

Distinguished In Uniform: Self Attention Vs. Virtual Nodes

Graph Transformers (GTs) such as SAN and GPS are graph processing models that combine Message-Passing GNNs (MPGNNs) with global Self-Attention. They were shown to be universal function approximators, with two reservations: 1. The initial node features must be augmented with certain positional encodings. 2. The approximation is non-uniform: Graphs of different sizes may require a different approximating network. We first clarify that this form of universality is not unique to GTs: Using the same positional encodings, also pure MPGNNs and even 2-layer MLPs are non-uniform universal approximators. We then consider uniform expressivity: The target function is to be approximated by a single network for graphs of all sizes. There, we compare GTs to the more efficient MPGNN + Virtual Node architecture. The essential difference between the two model definitions is in their global computation method -- Self-Attention Vs Virtual Node. We prove that none of the models is a uniform-universal approximator, before proving our main result: Neither model's uniform expressivity subsumes the other's. We demonstrate the theory with experiments on synthetic data. We further augment our study with real-world datasets, observing mixed results which indicate no clear ranking in practice as well.

cs.LG↗

arXiv2024

End-to-End Reinforcement Learning of Curative Curtailment with Partial Measurement Availability

In the course of the energy transition, the expansion of generation and consumption will change, and many of these technologies, such as PV systems, electric cars and heat pumps, will influence the power flow, especially in the distribution grids. Scalable methods that can make decisions for each grid connection are needed to enable congestion-free grid operation in the distribution grids. This paper presents a novel end-to-end approach to resolving congestion in distribution grids with deep reinforcement learning. Our architecture learns to curtail power and set appropriate reactive power to determine a non-congested and, thus, feasible grid state. State-of-the-art methods such as the optimal power flow (OPF) demand high computational costs and detailed measurements of every bus in a grid. In contrast, the presented method enables decisions under sparse information with just some buses observable in the grid. Distribution grids are generally not yet fully digitized and observable, so this method can be used for decision-making on the majority of low-voltage grids. On a real low-voltage grid the approach resolves 100\% of violations in the voltage band and 98.8\% of asset overloads. The results show that decisions can also be made on real grids that guarantee sufficient quality for congestion-free grid operation.

cs.LG↗

arXiv2024

Are Targeted Messages More Effective?

Graph neural networks (GNN) are deep learning architectures for graphs. Essentially, a GNN is a distributed message passing algorithm, which is controlled by parameters learned from data. It operates on the vertices of a graph: in each iteration, vertices receive a message on each incoming edge, aggregate these messages, and then update their state based on their current state and the aggregated messages. The expressivity of GNNs can be characterised in terms of certain fragments of first-order logic with counting and the Weisfeiler-Lehman algorithm. The core GNN architecture comes in two different versions. In the first version, a message only depends on the state of the source vertex, whereas in the second version it depends on the states of the source and target vertices. In practice, both of these versions are used, but the theory of GNNs so far mostly focused on the first one. On the logical side, the two versions correspond to two fragments of first-order logic with counting that we call modal and guarded. The question whether the two versions differ in their expressivity has been mostly overlooked in the GNN literature and has only been asked recently (Grohe, LICS'23). We answer this question here. It turns out that the answer is not as straightforward as one might expect. By proving that the modal and guarded fragment of first-order logic with counting have the same expressivity over labelled undirected graphs, we show that in a non-uniform setting the two GNN versions have the same expressivity. However, we also prove that in a uniform setting the second version is strictly more expressive.

cs.LO↗

arXiv2024

Future Directions in the Theory of Graph Machine Learning

Machine learning on graphs, especially using graph neural networks (GNNs), has seen a surge in interest due to the wide availability of graph data across a broad spectrum of disciplines, from life to social and engineering sciences. Despite their practical success, our theoretical understanding of the properties of GNNs remains highly incomplete. Recent theoretical advancements primarily focus on elucidating the coarse-grained expressive power of GNNs, predominantly employing combinatorial techniques. However, these studies do not perfectly align with practice, particularly in understanding the generalization behavior of GNNs when trained with stochastic first-order optimization techniques. In this position paper, we argue that the graph machine learning community needs to shift its attention to developing a balanced theory of graph machine learning, focusing on a more thorough understanding of the interplay of expressive power, generalization, and optimization.

cs.LG↗