Transformers from Diffusion: A Unified Framework for Neural Message Passing
Bibliographic record
Abstract
Learning representations for structured data with certain geometries (e.g., observed or unobserved) is a fundamental challenge, wherein message passing neural networks (MPNNs) have become a de facto class of model solutions. In this paper, inspired by physical systems, we propose an energy-constrained diffusion model, which integrates the inductive bias of diffusion on manifolds with layer-wise constraints of energy minimization. We identify that the diffusion operators have a one-to-one correspondence with the energy functions implicitly descended by the diffusion process, and the finite-difference iteration for solving the energy-constrained diffusion system induces the propagation layers of various types of MPNNs operating on observed or latent structures. This leads to a unified mathematical framework for common neural architectures whose computational flows can be cast as message passing (or its special case), including MLPs, GNNs, and Transformers. Building on these insights, we devise a new class of neural message passing models, dubbed diffusion-inspired Transformers (DIFFormer), whose global attention layers are derived from the principled energy-constrained diffusion framework. Across diverse datasets ranging from real-world networks to images, texts, and physical particles, we demonstrate that the new model achieves promising performance in scenarios where the data structures are observed (as a graph), partially observed, or entirely unobserved.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.005 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.002 |
| Scholarly communication | 0.002 | 0.005 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".