GraphXForm: Graph transformer for computer-aided molecular design with application to extraction

Generative deep learning has become pivotal in molecular design for drug discovery and materials science. 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 with self-improvement learning from language modeling, allowing stable fine-tuning of deep transformers with many layers. We evaluate GraphXForm on two solvent design tasks for liquid-liquid extraction, showing that it outperforms four state-of-the-art molecular design techniques, while it can flexibly enforce structural constraints or initiate the design from existing molecular structures.

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.

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.

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.

Future Directions in Foundations 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 more balanced theory of graph machine learning, focusing on a more thorough understanding of the interplay of expressive power, generalization, and optimization.

Selecting Walk Schemes for Database Embedding

Machinery for data analysis often requires a numeric representation of the input. Towards that, a common practice is to embed components of structured data into a high-dimensional vector space. We study the embedding of the tuples of a relational database, where existing techniques are often based on optimization tasks over a collection of random walks from the database. The focus of this paper is on the recent FoRWaRD algorithm that is designed for dynamic databases, where walks are sampled by following foreign keys between tuples. Importantly, different walks have different schemas, or "walk schemes", that are derived by listing the relations and attributes along the walk. Also importantly, different walk schemes describe relationships of different natures in the database. We show that by focusing on a few informative walk schemes, we can obtain tuple embedding significantly faster, while retaining the quality. We define the problem of scheme selection for tuple embedding, devise several approaches and strategies for scheme selection, and conduct a thorough empirical study of the performance over a collection of downstream tasks. Our results confirm that with effective strategies for scheme selection, we can obtain high-quality embeddings considerably (e.g., three times) faster, preserve the extensibility to newly inserted tuples, and even achieve an increase in the precision of some tasks.

Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark

The recent Long-Range Graph Benchmark (LRGB, Dwivedi et al. 2022) introduced a set of graph learning tasks strongly dependent on long-range interaction between vertices. Empirical evidence suggests that on these tasks Graph Transformers significantly outperform Message Passing GNNs (MPGNNs). In this paper, we carefully reevaluate multiple MPGNN baselines as well as the Graph Transformer GPS (Ramp\'a\v{s}ek et al. 2022) on LRGB. Through a rigorous empirical analysis, we demonstrate that the reported performance gap is overestimated due to suboptimal hyperparameter choices. It is noteworthy that across multiple datasets the performance gap completely vanishes after basic hyperparameter optimization. In addition, we discuss the impact of lacking feature normalization for LRGB's vision datasets and highlight a spurious implementation of LRGB's link prediction metric. The principal aim of our paper is to establish a higher standard of empirical rigor within the graph machine learning community.

Structural Node Embeddings with Homomorphism Counts

Graph homomorphism counts, first explored by Lov\'asz in 1967, have recently garnered interest as a powerful tool in graph-based machine learning. Grohe (PODS 2020) proposed the theoretical foundations for using homomorphism counts in machine learning on graph level as well as node level tasks. By their very nature, these capture local structural information, which enables the creation of robust structural embeddings. While a first approach for graph level tasks has been made by Nguyen and Maehara (ICML 2020), we experimentally show the effectiveness of homomorphism count based node embeddings. Enriched with node labels, node weights, and edge weights, these offer an interpretable representation of graph data, allowing for enhanced explainability of machine learning models. We propose a theoretical framework for isomorphism-invariant homomorphism count based embeddings which lend themselves to a wide variety of downstream tasks. Our approach capitalises on the efficient computability of graph homomorphism counts for bounded treewidth graph classes, rendering it a practical solution for real-world applications. We demonstrate their expressivity through experiments on benchmark datasets. Although our results do not match the accuracy of state-of-the-art neural architectures, they are comparable to other advanced graph learning models. Remarkably, our approach demarcates itself by ensuring explainability for each individual feature. By integrating interpretable machine learning algorithms like SVMs or Random Forests, we establish a seamless, end-to-end explainable pipeline. Our study contributes to the advancement of graph-based techniques that offer both performance and interpretability.

The Descriptive Complexity of Graph Neural Networks

We analyse the power of graph neural networks (GNNs) in terms of Boolean circuit complexity and descriptive complexity. We prove that the graph queries that can be computed by a polynomial-size bounded-depth family of GNNs are exactly those definable in the guarded fragment GFO+C of first-order logic with counting and with built-in relations. This puts GNNs in the circuit complexity class TC^0. Remarkably, the GNN families may use arbitrary real weights and a wide class of activation functions that includes the standard ReLU, logistic "sigmoid", and hyperbolic tangent functions. If the GNNs are allowed to use random initialisation and global readout (both standard features of GNNs widely used in practice), they can compute exactly the same queries as bounded depth Boolean circuits with threshold gates, that is, exactly the queries in TC^0. Moreover, we show that queries computable by a single GNN with piecewise linear activations and rational weights are definable in GFO+C without built-in relations. Therefore, they are contained in uniform TC^0.

Some Might Say All You Need Is Sum

The expressivity of Graph Neural Networks (GNNs) is dependent on the aggregation functions they employ. Theoretical works have pointed towards Sum aggregation GNNs subsuming every other GNNs, while certain practical works have observed a clear advantage to using Mean and Max. An examination of the theoretical guarantee identifies two caveats. First, it is size-restricted, that is, the power of every specific GNN is limited to graphs of a certain maximal size. Successfully processing larger graphs may require an other GNN, and so on. Second, it concerns the power to distinguish non-isomorphic graphs, not the power to approximate general functions on graphs, and the former does not necessarily imply the latter. It is important that a GNN's usability will not be limited to graphs of any certain maximal size. Therefore, we explore the realm of unrestricted-size expressivity. We prove that simple functions, which can be computed exactly by Mean or Max GNNs, are inapproximable by any Sum GNN. We prove that under certain restrictions, every Mean or Max GNNs can be approximated by a Sum GNN, but even there, a combination of (Sum, [Mean/Max]) is more expressive than Sum alone. Lastly, we prove further expressivity limitations of Sum-GNNs.