Text-based de novo Molecule Generation

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

1 leaderboard table shown for this task, 1 with rows (a “benchmark” on this site is a table with at least one row, as on /sota), ordered by row count. “Best model” is the first row in the archive's own order at snapshot; nothing is re-ranked here and metric direction is not recorded in the archive. PwC's Trend sparklines are not in the archive, so that column is omitted.

Syntology column: samples harvested from the paper's repositories and executed on synthesized fixtures; “ran” is not a correctness claim and does not order the table. A dash means no Syntology record for that paper, not a recorded non-run. Read from the graph 2026-09-24.

Libraries

Not in the archive: the export carries no per-task library table, so there is nothing to show at snapshot 2025-07-28.

Datasets archive 2025-07-28

3 datasets whose archive record lists this task, ordered by the archive's paper count.

Subtasks archive 2025-07-28

No subtask under this task in the archive's task tree.

Parent tasks archive 2025-07-28

Most implemented papers archive 2025-07-28

13 shown of 13 papers with code (14 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• MolFM: A Multimodal Molecular Foundation Model
  6 Jun 2023 2 repositories listed
  In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs.
• Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language
  10 Feb 2025 1 repository listed
  Recent advancements in AI for biological research focus on integrating molecular data with natural language to accelerate drug discovery.
• Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces
  16 Dec 2024 1 repository listed
  Generating novel molecules with higher properties than the training space, namely the out-of-distribution generation, is important for de novo drug design.
• A Bayesian Flow Network Framework for Chemistry Tasks
  28 Jul 2024 1 repository listed
  In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data.
• LDMol: Text-to-Molecule Diffusion Model with Structurally Informative Latent Space
  28 May 2024 1 repository listed Syntology ran 6 of 9 samples · 3 unverified · 1 pointer-only (licence)
  With the emergence of diffusion models as the frontline of generative models, many researchers have proposed molecule generation techniques with conditional diffusion models.
• BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning
  27 Feb 2024 1 repository listed
  However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.
• Text-Guided Molecule Generation with Diffusion Language Model
  20 Feb 2024 1 repository listed Syntology ran 14 of 21 samples · 7 unverified · 21 pointer-only (licence)
  In this work, we propose the Text-Guided Molecule Generation with Diffusion Language Model (TGM-DLM), a novel approach that leverages diffusion models to address the limitations of autoregressive methods.
• BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations
  11 Oct 2023 1 repository listed Syntology ran 1 of 1 samples · 0 unverified
  Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery.
• GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text
  14 Aug 2023 1 repository listed Syntology ran 1 of 1 samples · 0 unverified
  Large language models have made significant strides in natural language processing, enabling innovative applications in molecular science by processing textual representations of molecules.
• Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective
  11 Jun 2023 1 repository listed
  In this work, we propose a novel LLM-based framework (MolReGPT) for molecule-caption translation, where an In-Context Few-Shot Molecule Learning paradigm is introduced to empower molecule discovery with LLMs like…
• MolXPT: Wrapping Molecules with Text for Generative Pre-training
  18 May 2023 1 repository listed
  Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of…
• Unifying Molecular and Textual Representations via Multi-task Language Modelling
  29 Jan 2023 1 repository listed
  Here, we propose the first multi-domain, multi-task language model that can solve a wide range of tasks in both the chemical and natural language domains.
• Translation between Molecules and Natural Language
  25 Apr 2022 1 repository listed Syntology ran 0 of 5 samples · 5 unverified
  We present MolT5 - a self-supervised learning framework for pretraining models on a vast amount of unlabeled natural language text and molecule strings.

Syntology lines on 5 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced. Read from the graph 2026-09-24.