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Utilization of 16 Different Word Embedding Methods and 8 Large Language Models namely BigBird, LongFormer, RNAFormer, Generative Pre-trained Transformers (GPT), Heterogeneous Graph Transformer (HCT), Bidirectional Encoder Representations from Transformers (BERT), ESM-1b, and Transformer in Diverse RNA Sequence Analysis Pipelines based on a Variety of Machine and Deep Learning Algorithms such that RFC: Rotation Forest Algorithm, RF: Random Forest, CNN: Convolutional Neural Network, GNN: Graph Neural Network, XGBoost: Xtreme Gradient Boosting, MLP: Multilayer Perceptron, GCN: Graph Convolutional Network, LogR: Logistic Regression, LSTM: Long Short Term Memory, GBDT: Gradient Boosting Decision Trees, BiLSTM: Bidirectional Long Short Term Memory, SVM: Support Vector Machine, GBU: Gated Recurrent Unit, NB: Naive Bayes, NNRM: Neural Network Regression Model, DF: Deep Forest, ASLM: Adaptive subspace learning model, ERM: ElasticNet Regression Model, DNN: Deep Neural Network, HGCN: Hyper Graph Convolutional Network.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: Utilization of 16 Different Word Embedding Methods and 8 Large Language Models namely BigBird, LongFormer, RNAFormer, Generative Pre-trained Transformers (GPT), Heterogeneous Graph Transformer (HCT), Bidirectional Encoder Representations from Transformers (BERT), ESM-1b, and Transformer in Diverse RNA Sequence Analysis Pipelines based on a Variety of Machine and Deep Learning Algorithms such that RFC: Rotation Forest Algorithm, RF: Random Forest, CNN: Convolutional Neural Network, GNN: Graph Neural Network, XGBoost: Xtreme Gradient Boosting, MLP: Multilayer Perceptron, GCN: Graph Convolutional Network, LogR: Logistic Regression, LSTM: Long Short Term Memory, GBDT: Gradient Boosting Decision Trees, BiLSTM: Bidirectional Long Short Term Memory, SVM: Support Vector Machine, GBU: Gated Recurrent Unit, NB: Naive Bayes, NNRM: Neural Network Regression Model, DF: Deep Forest, ASLM: Adaptive subspace learning model, ERM: ElasticNet Regression Model, DNN: Deep Neural Network, HGCN: Hyper Graph Convolutional Network.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Sequencing, Plasmid Preparation

A Summary of 8 Contemporary Language Models utilized in RNA Sequence Analysis tasks.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: A Summary of 8 Contemporary Language Models utilized in RNA Sequence Analysis tasks.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Sequencing, Blocking Assay

Summary of open-source language models based predictors in existing studies.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: Summary of open-source language models based predictors in existing studies.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Binding Assay, Biomarker Discovery, Modification, RNA Structure Prediction, Gene Expression, CRISPR, Methylation

Summary of Uniquely Pre-trained Language Models along with pre-training Data for RNA Sequence Analysis Tasks.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: Summary of Uniquely Pre-trained Language Models along with pre-training Data for RNA Sequence Analysis Tasks.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Sequencing, Virus, Derivative Assay

Non-coding RNA target prediction related 4 distinct RNA sequence analysis tasks predictive pipelines performance.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: Non-coding RNA target prediction related 4 distinct RNA sequence analysis tasks predictive pipelines performance.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Sequencing, Control, Small Interfering RNA

RNA Interaction Prediction related 4 distinct RNA sequence analysis tasks predictive pipelines performance.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: RNA Interaction Prediction related 4 distinct RNA sequence analysis tasks predictive pipelines performance.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Sequencing, Droplet Countercurrent Chromatography, Binding Assay

RNA Subcellular Localization Prediction, RNA Sites Prediction, and Gene Analysis related 8 distinct RNA sequence analysis tasks predictive pipelines performance.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: RNA Subcellular Localization Prediction, RNA Sites Prediction, and Gene Analysis related 8 distinct RNA sequence analysis tasks predictive pipelines performance.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Sequencing, Alternative Splicing, Gene Expression

RNA Modification Prediction related 7 distinct RNA sequence analysis tasks predictive pipelines performance.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: RNA Modification Prediction related 7 distinct RNA sequence analysis tasks predictive pipelines performance.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: RNA modification, Sequencing, Modification, Methylation

RNA Function and Structure Prediction related 3 distinct RNA sequence analysis tasks predictive pipelines performance.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: RNA Function and Structure Prediction related 3 distinct RNA sequence analysis tasks predictive pipelines performance.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Sequencing, RNA Structure Prediction

RNA special characteristics analysis and single-cell analysis related 3 distinct RNA sequence analysis tasks predictive pipelines performance.

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: RNA special characteristics analysis and single-cell analysis related 3 distinct RNA sequence analysis tasks predictive pipelines performance.

Article Snippet: Danilevicz et al., 2023 , Long non coding RNA Prediction , BERT , BERT , Pre-train , https://github.com/AppliedBioinformatics/lncRNAPrediction_Interpretation.

Techniques: Single-cell Analysis, Sequencing, Biomarker Discovery