Recent advances in the Self-Referencing Embedding Strings (SELFIES) library
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Abstract (arXiv)
String-based molecular representations play a crucial role in cheminformatics applications, and with the growing success of deep learning in chemistry, have been readily adopted into machine learning pipelines. However, traditional string-based representations such as SMILES are often prone to syntactic and semantic errors when produced by generative models. To address these problems, a novel representation, SELF-referencIng Embedded Strings (SELFIES), was proposed that is inherently 100% robust, alongside an accompanying open-source implementation. Since then, we have generalized SELFIES to support a wider range of molecules and semantic constraints and streamlined its underlying grammar. We have implemented this updated representation in subsequent versions of selfieslib, where we have also made major advances with respect to design, efficiency, and supported features. Hence, we present the current status of selfieslib (version 2.1.1) in this manuscript.
Key facts. Cited by 8 papers in the map (data through 7 Oct 2026). Builds on 9 of its 26 references that are in the map. First posted on arXiv 7 Feb 2023.
Builds on
9 of 26 references.
References · 9
- 2016Automatic chemical design using a data-driven continuous representation of moleculescited by 762
- 2017Grammar Variational Autoencodercited by 283
- 2017Molecular De Novo Design through Deep Reinforcement Learningcited by 264
- 2017Deep Reinforcement Learning for De-Novo Drug Designcited by 161
- 2022SELFIES and the future of molecular string representationscited by 76
- 2022LIMO: Latent Inceptionism for Targeted Molecule Generationcited by 40
- 2022Group SELFIES: A Robust Fragment-Based Molecular String Representationcited by 32
- 2020Deep Molecular Dreaming: Inverse machine learning for de-novo molecular design and interpretability with surjective representationscited by 20
- 2020Curiosity in exploring chemical space: Intrinsic rewards for deep molecular reinforcement learningcited by 16
Built on by
Citing papers per year: 2023: 1; 2024: 2; 2025: 3; 2026: 2.
8 papers.
- 2023Explainability Techniques for Chemical Language Modelscited by 6
- 2024Tokenization for Molecular Foundation Modelscited by 4
- 2025A Genetic Algorithm for Navigating Synthesizable Molecular Spacescited by 4
- 2026Beyond Affinity: A Benchmark of 1D, 2D, and 3D Methods Reveals Critical Trade-offs in Structure-Based Drug Designcited by 2
- 2024Quantum Computing-Enhanced Algorithm Unveils Novel Inhibitors for KRAScited by 1
- 2026TSSR: Two-Stage Swap-Reward-Driven Reinforcement Learning for Character-Level SMILES Generationcited by 1
- 2025Multimodal Quantum Vision Transformer for Enzyme Commission Classification from Biochemical Representationscited by 0
- 2025General Intelligence-based Fragmentation (GIF): A framework for peak-labeled spectra simulationcited by 0
- 2026Beyond Affinity: A Benchmark of 1D, 2D, and 3D Methods Reveals Critical Trade-offs in Structure-Based Drug Design13 Jan 2026
- 2026TSSR: Two-Stage Swap-Reward-Driven Reinforcement Learning for Character-Level SMILES Generation8 Jan 2026
- 2025General Intelligence-based Fragmentation (GIF): A framework for peak-labeled spectra simulation11 Nov 2025
- 2025A Genetic Algorithm for Navigating Synthesizable Molecular Spaces25 Sep 2025
- 2025Multimodal Quantum Vision Transformer for Enzyme Commission Classification from Biochemical Representations20 Aug 2025
- 2024Tokenization for Molecular Foundation Models19 Sep 2024
- 2024Quantum Computing-Enhanced Algorithm Unveils Novel Inhibitors for KRAS13 Feb 2024
- 2023Explainability Techniques for Chemical Language Models25 May 2023