Papers › Molecular Generative Model Based On Adversarially Regularized Autoencoder

Molecular Generative Model Based On Adversarially Regularized Autoencoder

13 Nov 2019arXiv:1912.05617archive 2025-07-28

Seung Hwan Hong, Jaechang Lim, Seongok Ryu, Woo Youn Kim

Deep generative models are attracting great attention as a new promising approach for molecular design. All models reported so far are based on either variational autoencoder (VAE) or generative adversarial network (GAN). Here we propose a new type model based on an adversarially regularized autoencoder (ARAE). It basically uses latent variables like VAE, but the distribution of the latent variables is obtained by adversarial training like in GAN. The latter is intended to avoid both inappropriate approximation of posterior distribution in VAE and difficulty in handling discrete variables in GAN. Our benchmark study showed that ARAE indeed outperformed conventional models in terms of validity, uniqueness, and novelty per generated molecule. We also demonstrated successful conditional generation of drug-like molecules with ARAE for both cases of single and multiple properties control. As a potential real-world application, we could generate EGFR inhibitors sharing the scaffolds of known active molecules while satisfying drug-like conditions simultaneously.

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

5 samples harvested; 0 ran; 0 honoured the contract we drafted; 5 have 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: 0 of the 5 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 gicsaw/ARAE_SMILES. “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.

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