Synthyra
April 9, 2026
BlogDual Triangle Attention: Position Sense for Bidirectional Models
Dual Triangle Attention keeps bidirectional context while giving transformers a built-in directional signal.
- Attention
- Transformers
- Foundation Models
Research
Technical articles, manuscripts, and publication-ready research from Synthyra.
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- Annotation Vocabulary
- Atlas
- Attention
- Benchmarking
- Codons
- DSM
- Dataset Curation
- Drug Discovery
- Foundation Models
- Protein Design
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- Protein Language Models
- Protein Protein Interaction
- Protify
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Showing 11 of 11 items: 11 blogs, 0 papers
Research
October 24, 2025
BlogAccidental Taxonomists: When Protein Models Learn the Wrong Shortcut
Protein interaction models can look strong by learning species differences instead of interaction biology.
- Protein Protein Interaction
- Dataset Curation
- Atlas
October 10, 2025
BlogAtlas: Making Protein Screens Searchable
Atlas turns sequence-first protein models into searchable maps for interaction, ligand, and annotation work.
- Atlas
- Protein Protein Interaction
- Drug Discovery
- Protein Function
September 18, 2025
BlogSynteract-4: Interaction Prediction as Retrieval
Synteract-4 reframes protein-protein interaction prediction as sequence-only representation learning at proteome scale.
- Protein Protein Interaction
- Synteract
- Atlas
August 21, 2025
BlogProtify: Model Choice As An Experiment
Protify makes protein language model evaluation repeatable across tasks, datasets, and training strategies.
- Protify
- Benchmarking
- Protein Language Models
June 9, 2025
BlogDSM: Protein Generation with Masked Diffusion
DSM brings masked diffusion to protein sequences, linking representation learning with biologically grounded protein generation.
- Protein Generation
- DSM
- Protein Design
April 22, 2025
BlogSynteract2: The Next Stage in Protein Interaction Prediction
Synteract2 extends sequence-based interaction modeling toward affinity and binding-site prediction while keeping evaluation caveats explicit.
- Protein Protein Interaction
- Synteract
- Atlas
March 18, 2025
BlogTranslator: Broad Protein Annotation, Fast
Translator maps protein sequences into structured functional annotation hypotheses using the Annotation Vocabulary framework.
- Annotation Vocabulary
- Protein Function
- Atlas
July 30, 2024
BlogAnnotation Vocabulary: Teaching Protein Models the Language of Function
Annotation Vocabulary turns protein properties into a structured language, giving models a cleaner bridge between sequence, function, and design.
- Annotation Vocabulary
- Protein Function
- Atlas
September 15, 2023
BlogcdsBERT: Why Codons Still Matter for Protein AI
cdsBERT showed that protein models can learn useful biology by looking one layer earlier, at the codons that encode amino acids.
- Codons
- Protein Language Models
- Foundation Models
June 7, 2023
BlogSynteract: Predicting Protein Interactions from Sequence
Synteract showed that large protein language models could help predict protein-protein interactions from amino acid sequence alone.
- Protein Protein Interaction
- Synteract
- Atlas