Property Prediction

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

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Libraries

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Datasets archive 2025-07-28

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Most implemented papers archive 2025-07-28

30 shown of 352 papers with code (691 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.

• 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.
• Strategies for Pre-training Graph Neural Networks
  29 May 2019 11 repositories listed Syntology ran 10 of 14 samples · 4 unverified · 2 pointer-only (licence)
  Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training.
• Object-Centric Learning with Slot Attention
  26 Jun 2020 8 repositories listed Syntology ran 14 of 21 samples · 7 unverified · 7 pointer-only (licence)
  Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features.
• 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…
• Temporal Graph Benchmark for Machine Learning on Temporal Graphs
  3 Jul 2023 6 repositories listed Syntology ran 5 of 7 samples · 2 unverified
  We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs.
• InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization
  31 Jul 2019 5 repositories listed
  There are also some recent methods based on language models (e.
• Molecular Fingerprints Are Strong Models for Peptide Function Prediction
  29 Jan 2025 4 repositories listed
  We study the effectiveness of molecular fingerprints for peptide property prediction and demonstrate that domain-specific feature extraction from molecular graphs can outperform complex and computationally expensive…
• A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language
  12 Sep 2022 4 repositories listed Syntology ran 2 of 8 samples · 6 unverified · 2 pointer-only (licence)
  Although artificial intelligence (AI) has made significant progress in understanding molecules in a wide range of fields, existing models generally acquire the single cognitive ability from the single molecular modality.
• Analyzing Learned Molecular Representations for Property Prediction
  2 Apr 2019 4 repositories listed Syntology ran 3 of 15 samples · 12 unverified
  In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary…
• Conditional molecular design with deep generative models
  30 Apr 2018 4 repositories listed
  Although machine learning has been successfully used to propose novel molecules that satisfy desired properties, it is still challenging to explore a large chemical space efficiently.
• 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.
• A Text-guided Protein Design Framework
  9 Feb 2023 3 repositories listed Syntology ran 2 of 3 samples · 1 unverified · 1 pointer-only (licence)
  Current AI-assisted protein design mainly utilizes protein sequential and structural information.
• Isotropic Gaussian Processes on Finite Spaces of Graphs
  3 Nov 2022 3 repositories listed
  We propose a principled way to define Gaussian process priors on various sets of unweighted graphs: directed or undirected, with or without loops.
• Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs
  30 Sep 2021 3 repositories listed
  Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods.
• ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction
  19 Oct 2020 3 repositories listed Syntology ran 2 of 3 samples · 1 unverified
  GNNs and chemical fingerprints are the predominant approaches to representing molecules for property prediction.
• Self-Supervised Graph Transformer on Large-Scale Molecular Data
  18 Jun 2020 3 repositories listed
  We pre-train GROVER with 100 million parameters on 10 million unlabelled molecules -- the biggest GNN and the largest training dataset in molecular representation learning.
• DeeperGCN: All You Need to Train Deeper GCNs
  13 Jun 2020 3 repositories listed
  Graph Convolutional Networks (GCNs) have been drawing significant attention with the power of representation learning on graphs.
• GEOM: Energy-annotated molecular conformations for property prediction and molecular generation
  9 Jun 2020 3 repositories listed
  The Geometric Ensemble Of Molecules (GEOM) dataset contains conformers for 133, 000 species from QM9, and 317, 000 species with experimental data related to biophysics, physiology, and physical chemistry.
• MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-based Protein Structure Prediction
  10 May 2016 3 repositories listed
  Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics.
• Publishing Neural Networks in Drug Discovery Might Compromise Training Data Privacy
  22 Oct 2024 2 repositories listed Syntology ran 1 of 7 samples · 6 unverified · 6 pointer-only (licence)
  We use membership inference attacks, a common method to assess privacy that is largely unexplored in the context of drug discovery, to examine neural networks for molecular property prediction in a black-box setting.
• Scikit-fingerprints: easy and efficient computation of molecular fingerprints in Python
  18 Jul 2024 2 repositories listed
  In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics.
• Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees
  12 Jul 2024 2 repositories listed
  Generating novel molecules is challenging, with most representations leading to generative models producing many invalid molecules.
• The Role of Model Architecture and Scale in Predicting Molecular Properties: Insights from Fine-Tuning RoBERTa, BART, and LLaMA
  2 May 2024 2 repositories listed
  However, we observed that absolute validation loss is not a definitive indicator of model performance - contradicts previous research - at least for fine-tuning tasks: instead, model size plays a crucial role.
• Global Concept Explanations for Graphs by Contrastive Learning
  25 Apr 2024 2 repositories listed
  Overall, our results show promising capability to extract the underlying structure-property relationships for complex graph property prediction tasks.
• Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey
  3 Mar 2024 2 repositories listed
  The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology.
• Can Large Language Models Understand Molecules?
  5 Jan 2024 2 repositories listed
  Notably, LLaMA-based SMILES embeddings show results comparable to pre-trained models on SMILES in molecular prediction tasks and outperform the pre-trained models for the DDI prediction tasks.
• Higher-Order Equivariant Neural Networks for Charge Density Prediction in Materials
  8 Dec 2023 2 repositories listed Syntology ran 7 of 9 samples · 2 unverified
  The calculation of electron density distribution using density functional theory (DFT) in materials and molecules is central to the study of their quantum and macro-scale properties, yet accurate and efficient…
• Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning
  11 Nov 2023 2 repositories listed
  The versatility of multimodal deep learning holds tremendous promise for advancing scientific research and practical applications.
• Lo-Hi: Practical ML Drug Discovery Benchmark
  10 Oct 2023 2 repositories listed
  We analyzed modern benchmarks and showed that they are unrealistic and overoptimistic.
• On the Stability of Expressive Positional Encodings for Graphs
  4 Oct 2023 2 repositories listed Syntology ran 2 of 4 samples · 2 unverified · 1 pointer-only (licence)
  Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures.

Syntology lines on 13 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.