GEqTrain is presented, a configuration-driven framework that separates dataset semantics, model composition, and training objectives, and GEqDiff, a generative extension based on equivariant flow matching that aims to make equivariant modeling more reproducible, extensible, and reusable.
Abstract
Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific tasks, outputs, and training regimes. We present GEqTrain, a configuration-driven framework that separates dataset semantics, model composition, and training objectives. Raw data are mapped to typed node-, edge-, and graph-level fields, while model stacks, losses, and training workflows are assembled declaratively through Hydra configurations. A shared equivariant backbone and training infrastructure can therefore be retargeted to a new task primarily through configuration. We demonstrate this flexibility on three different problems handled within one software stack: coarse-grained-to-atomistic backmapping of biomolecular systems, prediction of NMR chemical shifts in molecular solids, and equivariant generative modeling. Our aim is not to surpass individually optimized task-specific systems, but to show that a shared representation and training infrastructure can achieve competitive accuracy across qualitatively different tasks at the cost of a configuration change. We further introduce GEqDiff, a generative extension based on equivariant flow matching. GEqDiff treats user-defined equivariant fields as first-class generation targets, jointly transporting Cartesian positions and non-scalar node fields spanning representations up to l=3 within a single equivariant flow. We validate this capability on a controlled synthetic benchmark inspired by protein secondary-structure motifs, showing that fields with heterogeneous transformation properties can be reconstructed jointly and with high fidelity. By reducing the software overhead of moving between predictive and generative, scalar and tensorial settings, GEqTrain aims to make equivariant modeling more reproducible, extensible, and reusable.
This paper proposes UniEdit, a Unified Graph-based Mixture-of-Experts (MoE) Molecular Editing model that offers a robust alternative to LLMs and incorporates a Mixture-of-Experts architecture that dynamically routes tasks to specialized components.
Jiajun Yu, Zhihao Wu, Yizhen Zheng et al.· Proceedings of the 32nd ACM...· 0 citations
We introduce Topoformer, a lightweight and scalable framework for graph representation learning that encodes topological structure into attention-friendly sequences. At the core of our method is Topo-Scan, a novel module that decomposes a graph into a short, ordered sequence of topological tokens by slicing over node or edge filtrations. These sequences capture multi-scale structural patterns, from local motifs to global organization, and are processed by a Transformer to produce expressive graph-level embeddings. Unlike traditional persistent homology pipelines, Topo-Scan is parallelizable, avoids costly diagram computations, and integrates seamlessly with standard deep learning architectures. We provide theoretical guarantees on the stability of our topological encodings and demonstrate state-of-the-art performance across graph classification and molecular property prediction benchmarks. Our results show that Topoformer matches or exceeds strong GNN and topology-based baselines while offering predictable and efficient compute. This work opens a new path for parallelizable and unifying approaches to graph representation learning that integrate topological inductive biases into attention frameworks.
Md Joshem Uddin, Astrit Tola, C. Akcora et al.· 0 citations
Circuit localization is a mechanistic interpretability task whose goal is to identify a sparse subgraph of a transformer's computation graph sufficient to reproduce a particular behavior. Most established methods localize circuits independently for each model--task pair. We instead frame circuit localization as a graph machine learning problem in which the edges of a computation graph represent computational pathways, and graph neural networks (GNNs) model interactions among these pathways. We introduce Graph Circuit Learning (GCL), a supervised, amortized framework that trains a GNN across multiple model--task pairs and applies it to unseen cases. To provide sufficient data, we augment the InterpBench benchmark with additional cases derived from the TracrBench programs. Of the 14 evaluated GCL configurations, the highest scored a median edge AUROC of $0.902$ (interquartile interval $[0.861, 0.942]$) on the 16 original held-out InterpBench cases. This is close to the published InterpBench median of $0.910$ for EAP-IG while remaining below ACDC's $0.959$. Removing all message-passing edges reduces the median to $0.825$. We also adapt PGExplainer, a GNN explainability method, to circuit localization, obtaining a median edge AUROC of $0.858$ on the same cases. These preliminary results suggest that graph machine learning offers a natural and potentially powerful perspective on circuit localization, and we hope this perspective encourages closer exchange between the two communities.
Chester Tan, Moritz Lampert, Courtney Maynard et al.· 0 citations
Transformer models for high-dimensional omics analysis process thousands of genes or pathways, although only a subset requires deep computation. Mixture-of-Recursions (MoR) improves efficiency through adaptive token-choice or expert-choice routing. We propose bioMoR, which, to the best of our knowledge, is the first framework to apply MoR to gene-level and pathway-level learning. Our contributions include identifying three locations for integrating structured biological knowledge within an MoR backbone: graph-based information sharing refines token embeddings, a structural bias guides self-attention toward biologically related tokens, and a graph-aware router uses neighborhood information to determine each token's recursion depth. These techniques are centered on our insight that additional knowledge of token interaction can effectively help models construct embeddings and select which tokens should be learned more deeply. Across eight benchmarks spanning diverse omics data types and evaluated under a unified five-fold cross-validation protocol, bioMoR improves average macro-F1 by 8.2 percentage points and balanced accuracy by 7.1 percentage points over the strongest biology-agnostic MoR baseline while using 75 percent fewer parameters and up to 58 percent fewer FLOPs than a non-recursive Transformer. The selected marker genes or pathways provide biological interpretability, while their token-specific recursion depths reveal how computation is allocated.
Koushik Howlader, Tirtho Roy, Md Tauhidul Islam et al.· 0 citations
Current AI protein structure prediction models involve multi-stage processing that combines deep neural networks with bioinformatics tools such as multiple sequence alignment (MSA). Researchers increasingly rely on intermediate or penultimate-layer activations from these models for downstream tasks including contact prediction, binding-site identification, and model interpretability. We describe the VizFold plugin, a modular framework that can be extended toward end-to-end composable pipelines. We demonstrate feasibility through standardized hook-based tracing for ESMFold and Boltz-2, archive validation, and reproducible deployment on an HPC cluster using managed caches, modules, quotas, and Slurm workflows. The framework extracts attention maps from user-selected layers and exports intermediate representations in a backend-specific run bundle (Boltz) or a canonical archive tree (ESMFold), with shared trace text conventions and explicit provenance metadata suitable for cross-model comparison. We provide step-by-step documentation for instrumentation and deployment so that other groups can reproduce or extend the pipeline on their own clusters. The framework and instrumentation code are open-source and available at https://github.com/AI2Science/vizfold-foundation.
Jayanth Vennamreddy, Arish Virani, Kevin Yin et al.· Practice and Experience in A...· 0 citations
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MIT News · Artificial Intelligence· news.mit.eduAug 18, 2026
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
