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README.md
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# LOGOS: Language of Generative Objects in Science
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<p align="center">
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<img src="pics/logos.png" alt="LOGOS" height="
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Unlike approaches that rely on natural language as an intermediary or require explicit 3D geometric networks, LOGOS operates directly on domain-native representations. Key spatial relationships (e.g., protein pocket–ligand contacts) are discretized and tokenized into the shared grammar, allowing the model to learn complex structural interactions in a purely sequential manner.
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<img src="pics/LOGOS-mainfigure.png" alt="LOGOS Framework Overview" width="
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### Key Features
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* **Pre-training & Downstream Alignment**: The grammar space ensures formal consistency between continued pre-training objectives and downstream task goals.
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<img src="pics/logos-data-process.png" alt="Data Construction in LOGOS" width="
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## Supported Tasks
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| Antibody CDR Design | Immunology | Design complementarity-determining regions for antibody engineering |
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<p align="center">
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<img src="pics/bench_comparison.png" alt="Benchmark Comparison" width="
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</p>
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## Model Architecture
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# LOGOS: Language of Generative Objects in Science
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<p align="center">
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<img src="pics/logos.png" alt="LOGOS" height="90">
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</p>
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<p align="center">
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Unlike approaches that rely on natural language as an intermediary or require explicit 3D geometric networks, LOGOS operates directly on domain-native representations. Key spatial relationships (e.g., protein pocket–ligand contacts) are discretized and tokenized into the shared grammar, allowing the model to learn complex structural interactions in a purely sequential manner.
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<p align="center">
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<img src="pics/LOGOS-mainfigure.png" alt="LOGOS Framework Overview" width="100%">
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</p>
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### Key Features
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* **Pre-training & Downstream Alignment**: The grammar space ensures formal consistency between continued pre-training objectives and downstream task goals.
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<p align="center">
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<img src="pics/logos-data-process.png" alt="Data Construction in LOGOS" width="100%">
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</p>
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## Supported Tasks
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| Antibody CDR Design | Immunology | Design complementarity-determining regions for antibody engineering |
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<p align="center">
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<img src="pics/bench_comparison.png" alt="Benchmark Comparison" width="100%">
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</p>
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## Model Architecture
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