mlsanityData to 7 Oct 2026

Deep Learning in Bioinformatics

arXiv 1603.06430 ↗First posted 21 Mar 2016cs.LG q-bio.GNcited by 48

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Abstract (arXiv)

In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e., omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e., deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies.

Key facts. Cited by 48 papers in the map (data through 7 Oct 2026). First posted on arXiv 21 Mar 2016.

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2021: 10; 2022: 7; 2023: 10; 2024: 12; 2025: 6; 2026: 3.

48 papers.

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  1. 2022A Survey on Generative Diffusion Modelcited by 238
  2. 2021Physics informed neural networks for continuum micromechanicscited by 46
  3. 2022gLaSDI: Parametric Physics-informed Greedy Latent Space Dynamics Identificationcited by 30
  4. 2024A Systematic Review of Intermediate Fusion in Multimodal Deep Learning for Biomedical Applicationscited by 25
  5. 2022Computer Vision and Deep Learning for Fish Classification in Underwater Habitats: A Surveycited by 14
  6. 2023SemiGNN-PPI: Self-Ensembling Multi-Graph Neural Network for Efficient and Generalizable Protein-Protein Interaction Predictioncited by 13
  7. 2024Physics-informed active learning with simultaneous weak-form latent space dynamics identificationcited by 13
  8. 2021BridgeDPI: A Novel Graph Neural Network for Predicting Drug-Protein Interactionscited by 12
  9. 2024Large Language Models in Plant Biologycited by 8
  10. 2021Calibrating multi-dimensional complex ODE from noisy data via deep neural networkscited by 6
  11. 2021Deep Algorithm Unrolling for Biomedical Imagingcited by 6
  12. 2021Deep learning models are not robust against noise in clinical textcited by 6
36 more
  1. 2023Structured and Fast Optimization: The Kronecker SGD Algorithmcited by 5
  2. 2025CP4SBI: Local Conformal Calibration of Credible Sets in Simulation-Based Inferencecited by 5
  3. 2022Deep Learning, Natural Language Processing, and Explainable Artificial Intelligence in the Biomedical Domaincited by 4
  4. 2023Divide-and-Conquer the NAS puzzle in Resource Constrained Federated Learning Systemscited by 3
  5. 2024Utilizing deep learning models for the identification of enhancers and super-enhancers based on genomic and epigenomic featurescited by 3
  6. 2024Comprehensive benchmarking of large language models for RNA secondary structure predictioncited by 3
  7. 2021SLA2P: Self-supervised Anomaly Detection with Adversarial Perturbationcited by 2
  8. 2021A Comprehensive Analytical Survey on Unsupervised and Semi-Supervised Graph Representation Learning Methodscited by 2
  9. 2023Physics-Informed Machine Learning of Argon Gas-Driven Melt Pool Dynamicscited by 2
  10. 2023Deep Learning in Computational Biology: Advancements, Challenges, and Future Outlookcited by 2
  11. 2024Deep Positive-Unlabeled Anomaly Detection for Contaminated Unlabeled Datacited by 2
  12. 2021Analysis of Vision-based Abnormal Red Blood Cell Classificationcited by 1
  13. 2021TargetNet: Functional microRNA Target Prediction with Deep Neural Networkscited by 1
  14. 2022SIBILA: A novel interpretable ensemble of general-purpose machine learning models applied to medical contextscited by 1
  15. 2022Towards Fine-Dining Recipe Generation with Generative Pre-trained Transformerscited by 1
  16. 2023Unpaired Image Translation to Mitigate Domain Shift in Liquid Argon Time Projection Chamber Detector Responsescited by 1
  17. 2023A One-Class Classifier for the Detection of GAN Manipulated Multi-Spectral Satellite Imagescited by 1
  18. 2024Exploring the Relationship: Transformative Adaptive Activation Functions in Comparison to Other Activation Functionscited by 1
  19. 2021Deep Metric Learning Model for Imbalanced Fault Diagnosiscited by 0
  20. 2022Optimization-Informed Neural Networkscited by 0
  21. 2023A Method for Detecting Murmurous Heart Sounds based on Self-similar Propertiescited by 0
  22. 2023A Matrix Ensemble Kalman Filter-based Multi-arm Neural Network to Adequately Approximate Deep Neural Networkscited by 0
  23. 2023Label Denoising through Cross-Model Agreementcited by 0
  24. 2024Predicting ATP binding sites in protein sequences using Deep Learning and Natural Language Processingcited by 0
  25. 2024OmniGenBench: Automating Large-scale in-silico Benchmarking for Genomic Foundation Modelscited by 0
  26. 2024From Epilepsy Seizures Classification to Detection: A Deep Learning-based Approach for Raw EEG Signalscited by 0
  27. 2024Integrating Secondary Structures Information into Triangular Spatial Relationships (TSR) for Advanced Protein Classificationcited by 0
  28. 2024DLSOM: A Deep learning-based strategy for liver cancer subtypingcited by 0
  29. 2025Exploration of Hepatitis B Virus Infection Dynamics through Physics-Informed Deep Learning Approachcited by 0
  30. 2025Transformers in Protein: A Surveycited by 0
  31. 2025CNN-LSTM Hybrid Model for AI-Driven Prediction of COVID-19 Severity from Spike Sequences and Clinical Datacited by 0
  32. 2025A HyperGraphMamba-Based Multichannel Adaptive Model for ncRNA Classificationcited by 0
  33. 2025Application of Deep Learning in Biological Data Compressioncited by 0
  34. 2026Neural quantum support vector data description for one-class classificationcited by 0
  35. 2026On Preserving Geometrical Invariance for Superpixel Image Classification using Graph Transformercited by 0
  36. 2026A Three-Way Testing Framework for Quantifying Epistemic Calibration Uncertainty in SBIcited by 0