mlsanityData to 7 Oct 2026

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction

arXiv 2004.11424 ↗First posted 23 Apr 2020q-bio.QM cs.LGcited by 63

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Abstract (arXiv)

Drug target interaction (DTI) prediction is a foundational task for in silico drug discovery, which is costly and time-consuming due to the need of experimental search over large drug compound space. Recent years have witnessed promising progress for deep learning in DTI predictions. However, the following challenges are still open: (1) the sole data-driven molecular representation learning approaches ignore the sub-structural nature of DTI, thus produce results that are less accurate and difficult to explain; (2) existing methods focus on limited labeled data while ignoring the value of massive unlabelled molecular data. We propose a Molecular Interaction Transformer (MolTrans) to address these limitations via: (1) knowledge inspired sub-structural pattern mining algorithm and interaction modeling module for more accurate and interpretable DTI prediction; (2) an augmented transformer encoder to better extract and capture the semantic relations among substructures extracted from massive unlabeled biomedical data. We evaluate MolTrans on real world data and show it improved DTI prediction performance compared to state-of-the-art baselines.

Key facts. Cited by 63 papers in the map (data through 7 Oct 2026). First posted on arXiv 23 Apr 2020.

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2021: 3; 2022: 6; 2023: 11; 2024: 13; 2025: 17; 2026: 13.

63 papers.

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  1. 2023BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associationscited by 100
  2. 2023Large AI Models in Health Informatics: Applications, Challenges, and the Futurecited by 61
  3. 2024BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuningcited by 54
  4. 2024DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaborationcited by 40
  5. 2022Interpretable bilinear attention network with domain adaptation improves drug-target predictioncited by 39
  6. 2023BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphscited by 24
  7. 2025AutoMind: Adaptive Knowledgeable Agent for Automated Data Sciencecited by 20
  8. 2023Transformers in Healthcare: A Surveycited by 17
  9. 2023Comprehensive evaluation of deep and graph learning on drug-drug interactions predictioncited by 10
  10. 2024Learning Molecular Representation in a Cellcited by 8
  11. 2022Hierarchical Graph Representation Learning for the Prediction of Drug-Target Binding Affinitycited by 7
  12. 2024A Cross-Field Fusion Strategy for Drug-Target Interaction Predictioncited by 5
38 more
  1. 2025Graph-structured Small Molecule Drug Discovery Through Deep Learning: Progress, Challenges, and Opportunitiescited by 5
  2. 2022Associative Learning Mechanism for Drug-Target Interaction Predictioncited by 4
  3. 2023Towards a more inductive world for drug repurposing approachescited by 4
  4. 2021Machine Learning Applications for Therapeutic Tasks with Genomics Datacited by 3
  5. 2022Graph neural networks and attention-based CNN-LSTM for protein classificationcited by 3
  6. 2023Single-Cell Multimodal Prediction via Transformerscited by 3
  7. 2024FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interactioncited by 3
  8. 2024FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learningcited by 3
  9. 2023FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretationcited by 2
  10. 2024Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Modelcited by 2
  11. 2024HiGraphDTI: Hierarchical Graph Representation Learning for Drug-Target Interaction Predictioncited by 2
  12. 2024Accurate Prediction of Ligand-Protein Interaction Affinities with Fine-Tuned Small Language Modelscited by 2
  13. 2024Scaling Structure Aware Virtual Screening to Billions of Molecules with SPRINTcited by 2
  14. 2025Drug-Target Interaction/Affinity Prediction: Deep Learning Models and Advances Reviewcited by 2
  15. 2025Clever Hans in Chemistry: Chemist Style Signals Confound Activity Prediction on Public Benchmarkscited by 2
  16. 2023PIGNet2: A Versatile Deep Learning-based Protein-Ligand Interaction Prediction Model for Binding Affinity Scoring and Virtual Screeningcited by 1
  17. 2024Benchmark on Drug Target Interaction Modeling from a Drug Structure Perspectivecited by 1
  18. 2025Inductive-Associative Meta-learning Pipeline with Human Cognitive Patterns for Unseen Drug-Target Interaction Predictioncited by 1
  19. 2026Tensor-DTI: Enhancing Biomolecular Interaction Prediction with Contrastive Embedding Learningcited by 1
  20. 2026A Systematic Survey and Benchmark of Deep Learning for Molecular Property Prediction in the Foundation Model Eracited by 1
  21. 2021CSI: Contrastive Data Stratification for Interaction Prediction and its Application to Compound-Protein Interaction Predictioncited by 0
  22. 2021AI-Bind: Improving Binding Predictions for Novel Protein Targets and Ligandscited by 0
  23. 2022Learning to Discover Medicinescited by 0
  24. 2022Infusing Linguistic Knowledge of SMILES into Chemical Language Modelscited by 0
  25. 2023Disentangling Node Attributes from Graph Topology for Improved Generalizability in Link Predictioncited by 0
  26. 2023Target-Free Compound Activity Prediction via Few-Shot Learningcited by 0
  27. 2024Barlow Twins Deep Neural Network for Advanced 1D Drug-Target Interaction Predictioncited by 0
  28. 2024A Heterogeneous Network-based Contrastive Learning Approach for Predicting Drug-Target Interactioncited by 0
  29. 2025Docking-Aware Attention: Dynamic Protein Representations through Molecular Context Integrationcited by 0
  30. 2025SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Predictioncited by 0
  31. 2025Addressing Model Overcomplexity in Drug-Drug Interaction Prediction With Molecular Fingerprintscited by 0
  32. 2025Heterogeneous network drug-target interaction prediction model based on graph wavelet transform and multi-level contrastive learningcited by 0
  33. 2025ModuLM: Enabling Modular and Multimodal Molecular Relational Learning with Large Language Modelscited by 0
  34. 2025KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Predictioncited by 0
  35. 2025Structure-Aware Contrastive Learning with Fine-Grained Binding Representations for Drug Discoverycited by 0
  36. 2025Learning to Align Molecules and Proteins: A Geometry-Aware Approach to Binding Affinitycited by 0
  37. 2025Attending on Multilevel Structure of Proteins enables Accurate Prediction of Cold-Start Drug-Target Interactionscited by 0
  38. 2025Oxytrees: Model Trees for Bipartite Learningcited by 0

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