BitterTranslate: A Natural Language Processing and Machine Learning-Based Framework for Mapping Bitter Taste Receptor Agonism
Bibliographic record
Abstract
Bitter taste receptors (TAS2Rs) are G protein-coupled receptors (GPCRs) expressed most notably on the tongue, but also in many extraoral tissues. TAS2R ligands are used for improving bitter-drug compliance, treating various illnesses, and studying the receptors' extraoral functions. Although machine learning, a promising drug discovery tool, can be used to predict TAS2R activators, obtaining high-quality features for training is time-intensive and reliant on specialized software. This work explores the potential of transformers (a neural network architecture for extracting features from sequential text strings that has revolutionized natural language processing-based tasks) for predicting these ligands. Hence, BitterTranslate, a TAS2R-agonist prediction algorithm, needs only the Simplified Molecular-Input Line-Entry System (SMILES) string of the ligand and the amino acid sequence of the TAS2R. The algorithm was built using two Bidirectional Encoder Representations from Transformers (BERT) models: one trained on small molecules to extract ligand features and the other trained on GPCRs to extract receptor features. An XGBoost classifier was pretrained on a large GPCR-ligand data set and fine-tuned on the smaller TAS2R-ligand data set. BitterTranslate predicts ligand associations with 80% precision and 65% recall across all TAS2Rs and 83% precision and 88% recall for the receptor with the most data: TAS2R14.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".