Drug Discovery

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

28 leaderboard tables shown for this task, 28 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. 10 shown of 28 until expanded.

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

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

Subtasks archive 2025-07-28

3 subtasks in the archive's task tree.

Most implemented papers archive 2025-07-28

30 shown of 566 papers with code (1,337 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.

• Semi-Supervised Classification with Graph Convolutional Networks
  9 Sep 2016 55 repositories listed Syntology ran 31 of 58 samples · 27 unverified · 22 pointer-only (licence)
  We present a scalable approach for semi-supervised learning on graph-structured data that is based on an efficient variant of convolutional neural networks which operate directly on graphs.
• Neural Message Passing for Quantum Chemistry
  4 Apr 2017 20 repositories listed Syntology ran 3 of 3 samples · 0 unverified · 1 pointer-only (licence)
  Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science.
• Self-Normalizing Neural Networks
  8 Jun 2017 13 repositories listed Syntology ran 1 of 1 samples · 0 unverified
  We introduce self-normalizing neural networks (SNNs) to enable high-level abstract representations.
• Gated Graph Sequence Neural Networks
  17 Nov 2015 13 repositories listed Syntology ran 0 of 12 samples · 12 unverified
  Graph-structured data appears frequently in domains including chemistry, natural language semantics, social networks, and knowledge bases.
• Junction Tree Variational Autoencoder for Molecular Graph Generation
  12 Feb 2018 11 repositories listed Syntology ran 1 of 1 samples · 0 unverified
  We evaluate our model on multiple tasks ranging from molecular generation to optimization.
• Convolutional Networks on Graphs for Learning Molecular Fingerprints
  30 Sep 2015 8 repositories listed Syntology ran 0 of 26 samples · 26 unverified · 1 pointer-only (licence)
  We introduce a convolutional neural network that operates directly on graphs.
• Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond
  13 Jul 2023 7 repositories listed
  The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation…
• Molecule Attention Transformer
  19 Feb 2020 7 repositories listed Syntology ran 4 of 8 samples · 4 unverified · 1 pointer-only (licence)
  Designing a single neural network architecture that performs competitively across a range of molecule property prediction tasks remains largely an open challenge, and its solution may unlock a widespread use of deep…
• Heterogeneous networks in drug-target interaction prediction
  22 Apr 2025 6 repositories listed
  Prior to discussing papers, we briefly introduce the datasets commonly used with these methods and measurements to assess their performance.
• Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules
  28 Nov 2020 6 repositories listed Syntology ran 5 of 9 samples · 4 unverified · 9 pointer-only (licence)
  Many important tasks in chemistry revolve around molecules during reactions.
• Multi-Objective Molecule Generation using Interpretable Substructures
  8 Feb 2020 5 repositories listed Syntology ran 1 of 3 samples · 2 unverified
  These rationales are identified from molecules as substructures that are likely responsible for each property of interest.
• Neural Message Passing with Edge Updates for Predicting Properties of Molecules and Materials
  8 Jun 2018 5 repositories listed Syntology ran 4 of 22 samples · 18 unverified · 4 pointer-only (licence)
  Neural message passing on molecular graphs is one of the most promising methods for predicting formation energy and other properties of molecules and materials.
• An Overview of Multi-Task Learning in Deep Neural Networks
  15 Jun 2017 5 repositories listed Syntology ran 1 of 1 samples · 0 unverified
  Multi-task learning (MTL) has led to successes in many applications of machine learning, from natural language processing and speech recognition to computer vision and drug discovery.
• Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks
  5 Jan 2017 5 repositories listed Syntology ran 0 of 1 samples · 1 unverified
  In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target.
• DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback
  20 Nov 2024 4 repositories listed
  One promising algorithm is DrugGPT, a transformer-based model, that generates small molecules for input protein sequences.
• Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery
  4 Jun 2021 4 repositories listed Syntology ran 0 of 14 samples · 14 unverified
  We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a…
• Directional Message Passing for Molecular Graphs
  6 Mar 2020 4 repositories listed Syntology ran 1 of 10 samples · 9 unverified · 3 pointer-only (licence)
  Each message is associated with a direction in coordinate space.
• DeepDTA: Deep Drug-Target Binding Affinity Prediction
  30 Jan 2018 4 repositories listed
  The results show that the proposed deep learning based model that uses the 1D representations of targets and drugs is an effective approach for drug target binding affinity prediction.
• Development and evaluation of a deep learning model for protein-ligand binding affinity prediction
  19 Dec 2017 4 repositories listed
  Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process.
• Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences
  6 Nov 2024 3 repositories listed Syntology ran 3 of 29 samples · 26 unverified
  While Transformers have yielded impressive results, their quadratic runtime dependency on the sequence length complicates their use for long genomic sequences and in-context learning on proteins and chemical sequences.
• Generative Flows on Synthetic Pathway for Drug Design
  6 Oct 2024 3 repositories listed Syntology ran 1 of 3 samples · 2 unverified
  This enables RxnFlow to learn generative flows over extensive action spaces comprising combinations of 1.
• Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers
  7 Feb 2024 3 repositories listed Syntology ran 10 of 13 samples · 3 unverified
  We also obtain SOTA results on QM9, MOLPCBA, and LIT-PCBA molecular property prediction benchmarks via transfer learning.
• ShennongAlpha: an AI-driven sharing and collaboration platform for intelligent curation, acquisition, and translation of natural medicinal material knowledge
  27 Dec 2023 3 repositories listed Syntology ran 2 of 2 samples · 0 unverified
  Natural Medicinal Materials (NMMs) have a long history of global clinical applications and a wealth of records and knowledge.
• TacoGFN: Target-conditioned GFlowNet for Structure-based Drug Design
  5 Oct 2023 3 repositories listed Syntology ran 6 of 10 samples · 4 unverified · 1 pointer-only (licence)
  We design TacoGFN, a novel GFlowNet-based approach for structure-based drug design, which can generate molecules conditioned on any protein pocket structure with probabilities proportional to its affinity and property…
• PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling
  1 Oct 2023 3 repositories listed Syntology ran 8 of 8 samples · 0 unverified
  Different pre-screening methods have been developed for rapid screening, but there is still a lack of structure-based methods applicable to various proteins that perform protein-ligand binding conformation prediction…
• ChemCrow: Augmenting large-language models with chemistry tools
  11 Apr 2023 3 repositories listed Syntology ran 1 of 3 samples · 2 unverified
  Our agent autonomously planned and executed the syntheses of an insect repellent, three organocatalysts, and guided the discovery of a novel chromophore.
• A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications
  16 Feb 2022 3 repositories listed
  Pretrained Language Models (PLMs) such as BERT have revolutionized the landscape of Natural Language Processing (NLP).
• Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphs
  11 Feb 2022 3 repositories listed Syntology ran 1 of 1 samples · 0 unverified
  Despite recent success in using the invariance principle for out-of-distribution (OOD) generalization on Euclidean data (e.
• DebiasedDTA: A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models
  4 Jul 2021 3 repositories listed
  Here, we present DebiasedDTA, a novel drug-target affinity (DTA) prediction model training framework that addresses dataset biases to improve the generalizability of affinity prediction models.
• Molecule Generation by Principal Subgraph Mining and Assembling
  29 Jun 2021 3 repositories listed Syntology ran 2 of 6 samples · 4 unverified
  Molecule generation is central to a variety of applications.

Syntology lines on 23 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.