Papers › Extracting Interpretable Logic Rules from Graph Neural Networks

Extracting Interpretable Logic Rules from Graph Neural Networks

25 Mar 2025arXiv:2503.19476archive 2025-07-28

Chuqin Geng, Zhaoyue Wang, Ziyu Zhao, Haolin Ye, Xujie Si

Graph neural networks (GNNs) operate over both input feature spaces and combinatorial graph structures, making it challenging to understand the rationale behind their predictions. As GNNs gain widespread popularity and demonstrate success across various domains, such as drug discovery, studying their interpretability has become a critical task. To address this, many explainability methods have been proposed, with recent efforts shifting from instance-specific explanations to global concept-based explainability. However, these approaches face several limitations, such as relying on predefined concepts and explaining only a limited set of patterns. To address this, we propose a novel framework, LOGICXGNN, for extracting interpretable logic rules from GNNs. LOGICXGNN is model-agnostic, efficient, and data-driven, eliminating the need for predefined concepts. More importantly, it can serve as a rule-based classifier and even outperform the original neural models. Its interpretability facilitates knowledge discovery, as demonstrated by its ability to extract detailed and accurate chemistry knowledge that is often overlooked by existing methods. Another key advantage of LOGICXGNN is its ability to generate new graph instances in a controlled and transparent manner, offering significant potential for applications such as drug design. We empirically demonstrate these merits through experiments on real-world datasets such as MUTAG and BBBP.

Code

Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.

Code Syntology ran Syntology

7 samples harvested; 6 ran; 0 honoured the contract we drafted; 1 has no recorded run. Read from Syntology's graph 2026-09-24; that is when this build read the record, not when the samples ran.

Licence: 7 of the 7 samples are pointer only, meaning Syntology does not serve that copy's text. This page shows no code text for any sample; each one links to its file in the repository.

Harvested from allengeng123/LogicXGNN. “Ran” means the sample executed on a synthesized input. It does not mean the output is correct, and nothing here reproduces the paper's results. “Honoured” and “violated” refer to a contract Syntology drafted from the code itself; “our draft was wrong” and “fixture could not drive it” are failures of Syntology's instrument, not of the code.

Each sample ends with its code_sha256, Syntology's identity for that exact code. An agent fetches the stored sample with Syntology's MCP tool get_code(code_sha256="…") (how to connect); click an identity to copy that call.

Repository labels, per sample. official repository: The archive marks this repository official for the paper. named in the paper: The archive records that the paper mentions this repository; it is not marked official. community (archive-listed): In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper. found in paper text by Syntology: Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted. community: Not in the archive's code links for this paper; a community repository Syntology harvested. Samples from a repository marked official are listed first. Licence labels name the repository's licence as recorded at harvest. “Pointer only” means Syntology does not serve that copy's text, for one of four reasons: no licence file was found; the licence was not identified; the licence is recorded as permissive but that copy's record is not marked cleared; or the licence is outside the permissive list Syntology serves text under (MIT, Apache-2.0, BSD and similar). Some licences outside that list permit redistribution, such as WTFPL, and GPL-3.0 under its conditions; they are simply not on the list. Hover a licence label for the reason. File links open the file on GitHub at the default branch, which may have changed since the harvest.

Tasks

Results from the paper archive 2025-07-28

No leaderboard rows for this paper in the archive.

Methods

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections