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molecular representation

Papers archive 2025-07-28

archive papers tagged: 168 · with a code link: 87 · where Syntology ran a sample: 31 (29 with a run with no instrument failure, 2 where every run was a failure of Syntology's instrument) Syntology

Show: all tagged papersonly where code ran (31 of 168 tagged: 29 with a run with no instrument failure, 2 where every run was a failure of Syntology's instrument)

Page 2 of 2: papers 101 to 168 of 168, in archive order: by repositories listed in the archive (most first), then newest first, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers that list no repository come after every paper that lists one.

Papers without a page here are shown as plain text. A Syntology line reads “N ran (of which C constructed an object rather than computing a result; K with no instrument failure: H honoured, V violated, P with no contract checked; I where Syntology's instrument failed) · U unverified”; the figure “where Syntology's instrument failed” counts failures of Syntology's instrument, not of the code. When the archive marks a repository official for the paper, the line starts with that repository's state (the archive's flag, not a verdict on who wrote the code); hover it for the repositories the samples that ran came from. Abstracts are on each paper's page.

• SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision
  7 Dec 2024 0 repositories listed
• Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates
  2 Dec 2024 0 repositories listed
• E3STO: Orbital Inspired SE(3)-Equivariant Molecular Representation for Electron Density Prediction
  8 Oct 2024 0 repositories listed
• FARM: Functional Group-Aware Representations for Small Molecules
  2 Oct 2024 0 repositories listed
• FineMolTex: Towards Fine-grained Molecular Graph-Text Pre-training
  21 Sep 2024 0 repositories listed
• Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models
  19 Sep 2024 0 repositories listed
• Mayer-homology learning prediction of protein-ligand binding affinities
  23 Aug 2024 0 repositories listed
• Advancing Molecular Machine Learning Representations with Stereoelectronics-Infused Molecular Graphs
  8 Aug 2024 0 repositories listed
• GNN-SKAN: Harnessing the Power of SwallowKAN to Advance Molecular Representation Learning with GNNs
  2 Aug 2024 0 repositories listed
• Technical report: Improving the properties of molecules generated by LIMO
  20 Jul 2024 0 repositories listed
• Improving Performance Prediction of Electrolyte Formulations with Transformer-based Molecular Representation Model
  28 Jun 2024 0 repositories listed
• Explainable Molecular Property Prediction: Aligning Chemical Concepts with Predictions via Language Models
  25 May 2024 0 repositories listed
• UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning
  15 May 2024 0 repositories listed
• DrugLLM: Open Large Language Model for Few-shot Molecule Generation
  7 May 2024 0 repositories listed
• HiGraphDTI: Hierarchical Graph Representation Learning for Drug-Target Interaction Prediction
  16 Apr 2024 0 repositories listed
• Active Causal Learning for Decoding Chemical Complexities with Targeted Interventions
  5 Apr 2024 0 repositories listed
• An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning
  20 Feb 2024 0 repositories listed
• Revealing the Relationship Between Publication Bias and Chemical Reactivity with Contrastive Learning
  19 Feb 2024 0 repositories listed
• Graph Multi-Similarity Learning for Molecular Property Prediction
  31 Jan 2024 0 repositories listed
• Accelerating Black-Box Molecular Property Optimization by Adaptively Learning Sparse Subspaces
  2 Jan 2024 0 repositories listed
• Integrating Chemical Language and Molecular Graph in Multimodal Fused Deep Learning for Drug Property Prediction
  29 Dec 2023 0 repositories listed
• AdaMR: Adaptable Molecular Representation for Unified Pre-training Strategy
  28 Dec 2023 0 repositories listed
• MultiModal-Learning for Predicting Molecular Properties: A Framework Based on Image and Graph Structures
  28 Nov 2023 0 repositories listed
• GlycoNMR: Dataset and benchmarks for NMR chemical shift prediction of carbohydrates with graph neural networks
  28 Nov 2023 0 repositories listed
• PointGAT: A quantum chemical property prediction model integrating graph attention and 3D geometry
  8 Oct 2023 0 repositories listed
• A Comprehensive Review of Generative AI in Healthcare
  1 Oct 2023 0 repositories listed
• 3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information
  28 Sep 2023 0 repositories listed
• 3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation
  8 Sep 2023 0 repositories listed
• Geometry-aware Line Graph Transformer Pre-training for Molecular Property Prediction
  1 Sep 2023 0 repositories listed
• Synergistic Fusion of Graph and Transformer Features for Enhanced Molecular Property Prediction
  25 Aug 2023 0 repositories listed
• May the Force be with You: Unified Force-Centric Pre-Training for 3D Molecular Conformations
  24 Aug 2023 0 repositories listed
• Multimodal Molecular Pretraining via Modality Blending
  12 Jul 2023 0 repositories listed
• MolCAP: Molecular Chemical reActivity pretraining and prompted-finetuning enhanced molecular representation learning
  13 Jun 2023 0 repositories listed
• Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations
  2 Jun 2023 0 repositories listed
• Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning
  22 May 2023 0 repositories listed
• Mol-PECO: a deep learning model to predict human olfactory perception from molecular structures
  21 May 2023 0 repositories listed
• Generation of 3D Molecules in Pockets via Language Model
  17 May 2023 0 repositories listed
• Evaluating the roughness of structure-property relationships using pretrained molecular representations
  14 May 2023 0 repositories listed
• Knowledge graph-enhanced molecular contrastive learning with functional prompt
  4 May 2023 0 repositories listed
• HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations
  27 Mar 2023 0 repositories listed
• Molecular Property Prediction by Semantic-invariant Contrastive Learning
  13 Mar 2023 0 repositories listed
• Molecular design method based on novel molecular representation and variational auto-encoder
  20 Feb 2023 0 repositories listed
• Persistent Dirac for molecular representation
  5 Feb 2023 0 repositories listed
• MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular Representation Learning
  20 Dec 2022 0 repositories listed
• Molecular Joint Representation Learning via Multi-modal Information
  25 Nov 2022 0 repositories listed
• A 3D-Shape Similarity-based Contrastive Approach to Molecular Representation Learning
  3 Nov 2022 0 repositories listed
• Substructure-Atom Cross Attention for Molecular Representation Learning
  15 Oct 2022 0 repositories listed
• Does GNN Pretraining Help Molecular Representation?
  13 Jul 2022 0 repositories listed
• Hyperbolic Molecular Representation Learning for Drug Repositioning
  6 Jul 2022 0 repositories listed
• Pre-training Transformers for Molecular Property Prediction Using Reaction Prediction
  6 Jul 2022 0 repositories listed
• 3D Graph Contrastive Learning for Molecular Property Prediction
  31 May 2022 0 repositories listed
• Associative Learning Mechanism for Drug-Target Interaction Prediction
  24 May 2022 0 repositories listed
• Learning multi-scale functional representations of proteins from single-cell microscopy data
  24 May 2022 0 repositories listed
• Attention-wise masked graph contrastive learning for predicting molecular property
  2 May 2022 0 repositories listed
• GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules
  12 Jan 2022 0 repositories listed
• Deep Molecular Representation Learning via Fusing Physical and Chemical Information
  28 Nov 2021 0 repositories listed
• Image-Like Graph Representations for Improved Molecular Property Prediction
  20 Nov 2021 0 repositories listed
• Multilingual Molecular Representation Learning via Contrastive Pre-training
  18 Sep 2021 0 repositories listed
• ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction
  11 Jun 2021 0 repositories listed
• Knowledge-aware Contrastive Molecular Graph Learning
  24 Mar 2021 0 repositories listed
• Conformation-Guided Molecular Representation with Hamiltonian Neural Networks
  1 Jan 2021 0 repositories listed
• Reprogramming Language Models for Molecular Representation Learning
  7 Dec 2020 0 repositories listed
• Directed Graph Attention Neural Network Utilizing 3D Coordinates for Molecular Property Prediction
  1 Dec 2020 0 repositories listed
• Neural networks and kernel ridge regression for excited states dynamics of CH₂NH₂^+: From single-state to multi-state representations and multi-property machine learning models
  18 Dec 2019 0 repositories listed
• Generative Models for Automatic Chemical Design
  2 Jul 2019 0 repositories listed
• Towards Interpretable Sparse Graph Representation Learning with Laplacian Pooling
  28 May 2019 0 repositories listed
• Step Change Improvement in ADMET Prediction with PotentialNet Deep Featurization
  28 Mar 2019 0 repositories listed
• Meta-QSAR: a large-scale application of meta-learning to drug design and discovery
  12 Sep 2017 0 repositories listed