Deconstructing equivariant representations in molecular systems

Recent equivariant models have shown significant progress in not just chemical property prediction, but as surrogates for dynamical simulations of molecules and materials. Many of the top performing models in this category are built within the framework of tensor products, which preserves equivariance by restricting interactions and transformations to those that are allowed by symmetry selection rules. Despite being a core part of the modeling process, there has not yet been much attention into understanding what information persists in these equivariant representations, and their general behavior outside of benchmark metrics. In this work, we report on a set of experiments using a simple equivariant graph convolution model on the QM9 dataset, focusing on correlating quantitative performance with the resulting molecular graph embeddings. Our key finding is that, for a scalar prediction task, many of the irreducible representations are simply ignored during training -- specifically those pertaining to vector ($l=1$) and tensor quantities ($l=2$) -- an issue that does not necessarily make itself evident in the test metric. We empirically show that removing some unused orders of spherical harmonics improves model performance, correlating with improved latent space structure. We provide a number of recommendations for future experiments to try and improve efficiency and utilization of equivariant features based on these observations.

One Model, Any Conjunctive Query: Graph Neural Networks for Answering Complex Queries over Knowledge Graphs

Traditional query answering over knowledge graphs -- or broadly over relational data -- is one of the most fundamental problems in data management. 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 work, we propose AnyCQ, a graph neural network model that can classify answers to any conjunctive query on any knowledge graph, following training. At the core of our framework lies a graph neural network model trained using a reinforcement learning objective to answer Boolean queries. Our approach and problem setup differ from existing query answering studies in multiple dimensions. First, we focus on the problem of query answer classification: given a query and a set of possible answers, classify these proposals as true or false relative to the complete knowledge graph. Second, we study the problem of query answer retrieval: given a query, retrieve an answer to the query relative to the complete knowledge graph or decide that no correct solutions exist. Trained on simple, small instances, AnyCQ can generalize to large queries of arbitrary structure, reliably classifying and retrieving answers to samples where existing approaches fail, which is empirically validated on new and challenging benchmarks. Furthermore, we demonstrate that our AnyCQ models effectively transfer to out-of-distribution knowledge graphs, when equipped with a relevant link predictor, highlighting their potential to serve as a general engine for query answering.

TGB 2.0: A Benchmark for Learning on Temporal Knowledge Graphs and Heterogeneous Graphs

Multi-relational temporal graphs are powerful tools for modeling real-world data, capturing the evolving and interconnected nature of entities over time. Recently, many novel models are proposed for ML on such graphs intensifying the need for robust evaluation and standardized benchmark datasets. However, the availability of such resources remains scarce and evaluation faces added complexity due to reproducibility issues in experimental protocols. To address these challenges, we introduce Temporal Graph Benchmark 2.0 (TGB 2.0), a novel benchmarking framework tailored for evaluating methods for predicting future links on Temporal Knowledge Graphs and Temporal Heterogeneous Graphs with a focus on large-scale datasets, extending the Temporal Graph Benchmark. TGB 2.0 facilitates comprehensive evaluations by presenting eight novel datasets spanning five domains with up to 53 million edges. TGB 2.0 datasets are significantly larger than existing datasets in terms of number of nodes, edges, or timestamps. In addition, TGB 2.0 provides a reproducible and realistic evaluation pipeline for multi-relational temporal graphs. Through extensive experimentation, we observe that 1) leveraging edge-type information is crucial to obtain high performance, 2) simple heuristic baselines are often competitive with more complex methods, 3) most methods fail to run on our largest datasets, highlighting the need for research on more scalable methods.

GraphAny: A Foundation Model for Node Classification on Any Graph

Foundation models that can perform inference on any new task without requiring specific training have revolutionized machine learning in vision and language applications. However, applications involving graph-structured data remain a tough nut for foundation models, due to challenges in the unique feature- and label spaces associated with each graph. Traditional graph ML models such as graph neural networks (GNNs) trained on graphs cannot perform inference on a new graph with feature and label spaces different from the training ones. Furthermore, existing models learn functions specific to the training graph and cannot generalize to new graphs. In this work, we tackle these two challenges with a new foundational architecture for inductive node classification named GraphAny. GraphAny models inference on a new graph as an analytical solution to a LinearGNN, thereby solving the first challenge. To solve the second challenge, we learn attention scores for each node to fuse the predictions of multiple LinearGNNs. Specifically, the attention module is carefully parameterized as a function of the entropy-normalized distance-features between multiple LinearGNNs predictions to ensure generalization to new graphs. Empirically, GraphAny trained on the Wisconsin dataset with only 120 labeled nodes can effectively generalize to 30 new graphs with an average accuracy of 67.26\% in an inductive manner, surpassing GCN and GAT trained in the supervised regime, as well as other inductive baselines.

FloorSet -- a VLSI Floorplanning Dataset with Design Constraints of Real-World SoCs

Floorplanning for systems-on-a-chip (SoCs) and its sub-systems is a crucial and non-trivial step of the physical design flow. It represents a difficult combinatorial optimization problem. A typical large scale SoC with 120 partitions generates a search-space of nearly 10E250. As novel machine learning (ML) approaches emerge to tackle such problems, there is a growing need for a modern benchmark that comprises a large training dataset and performance metrics that better reflect real-world constraints and objectives compared to existing benchmarks. To address this need, we present FloorSet -- two comprehensive datasets of synthetic fixed-outline floorplan layouts that reflect the distribution of real SoCs. Each dataset has 1M training samples and 100 test samples where each sample is a synthetic floor-plan. FloorSet-Prime comprises fully-abutted rectilinear partitions and near-optimal wire-length. A simplified dataset that reflects early design phases, FloorSet-Lite comprises rectangular partitions, with under 5 percent white-space and near-optimal wire-length. Both datasets define hard constraints seen in modern design flows such as shape constraints, edge-affinity, grouping constraints, and pre-placement constraints. FloorSet is intended to spur fundamental research on large-scale constrained optimization problems. Crucially, FloorSet alleviates the core issue of reproducibility in modern ML driven solutions to such problems. FloorSet is available as an open-source repository for the research community.

Zero-shot Logical Query Reasoning on any Knowledge Graph

Complex logical query answering (CLQA) in knowledge graphs (KGs) goes beyond simple KG completion and aims at answering compositional queries comprised of multiple projections and logical operations. Existing CLQA methods that learn parameters bound to certain entity or relation vocabularies can only be applied to the graph they are trained on which requires substantial training time before being deployed on a new graph. Here we present UltraQuery, an inductive reasoning model that can zero-shot answer logical queries on any KG. The core idea of UltraQuery is to derive both projections and logical operations as vocabulary-independent functions which generalize to new entities and relations in any KG. With the projection operation initialized from a pre-trained inductive KG reasoning model, UltraQuery can solve CLQA on any KG even if it is only finetuned on a single dataset. Experimenting on 23 datasets, UltraQuery in the zero-shot inference mode shows competitive or better query answering performance than best available baselines and sets a new state of the art on 14 of them.

Graph Foundation Models

Graph Foundation Model (GFM) is a new trending research topic in the graph domain, aiming to develop a graph model capable of generalizing across different graphs and tasks. However, a versatile GFM has not yet been achieved. The key challenge in building GFM is how to enable positive transfer across graphs with diverse structural patterns. Inspired by the existing foundation models in the CV and NLP domains, we propose a novel perspective for the GFM development by advocating for a "graph vocabulary", in which the basic transferable units underlying graphs encode the invariance on graphs. We ground the graph vocabulary construction from essential aspects including network analysis, theoretical foundations, and stability. Such a vocabulary perspective can potentially advance the future GFM design following the neural scaling laws.

Improving Compositional Generalization Using Iterated Learning and Simplicial Embeddings

Compositional generalization, the ability of an agent to generalize to unseen combinations of latent factors, is easy for humans but hard for deep neural networks. A line of research in cognitive science has hypothesized a process, ``iterated learning,'' to help explain how human language developed this ability; the theory rests on simultaneous pressures towards compressibility (when an ignorant agent learns from an informed one) and expressivity (when it uses the representation for downstream tasks). Inspired by this process, we propose to improve the compositional generalization of deep networks by using iterated learning on models with simplicial embeddings, which can approximately discretize representations. This approach is further motivated by an analysis of compositionality based on Kolmogorov complexity. We show that this combination of changes improves compositional generalization over other approaches, demonstrating these improvements both on vision tasks with well-understood latent factors and on real molecular graph prediction tasks where the latent structure is unknown.

Towards Foundation Models for Knowledge Graph Reasoning

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.

MatSciML: A Broad, Multi-Task Benchmark for Solid-State Materials Modeling

We propose MatSci ML, a novel benchmark for modeling MATerials SCIence using Machine Learning (MatSci ML) methods focused on solid-state materials with periodic crystal structures. Applying machine learning methods to solid-state materials is a nascent field with substantial fragmentation largely driven by the great variety of datasets used to develop machine learning models. This fragmentation makes comparing the performance and generalizability of different methods difficult, thereby hindering overall research progress in the field. Building on top of open-source datasets, including large-scale datasets like the OpenCatalyst, OQMD, NOMAD, the Carolina Materials Database, and Materials Project, the MatSci ML benchmark provides a diverse set of materials systems and properties data for model training and evaluation, including simulated energies, atomic forces, material bandgaps, as well as classification data for crystal symmetries via space groups. The diversity of properties in MatSci ML makes the implementation and evaluation of multi-task learning algorithms for solid-state materials possible, while the diversity of datasets facilitates the development of new, more generalized algorithms and methods across multiple datasets. In the multi-dataset learning setting, MatSci ML enables researchers to combine observations from multiple datasets to perform joint prediction of common properties, such as energy and forces. Using MatSci ML, we evaluate the performance of different graph neural networks and equivariant point cloud networks on several benchmark tasks spanning single task, multitask, and multi-data learning scenarios. Our open-source code is available at https://github.com/IntelLabs/matsciml.