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README.md
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extra_gated_fields:
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I agree to use this model for non-commercial use ONLY: checkbox
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---
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#
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This model ranks candidate disease-causing genes based on a patient’s phenotypic information. During inference, it does not generate a full free-text response. Instead, it performs gene-token subspace ranking on the logits at the final position and outputs a prioritized list of genes.
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> **Visit https://github.com/discostudy/phenogemini
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> for additional usage examples and demonstration data derived from real-world cohorts.**
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#
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Use `https://phenogemini.org` to generate a prompt that includes similar patients.
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#
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```python
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from transformers import AutoModelForCausalLM, AutoTokenizer
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import torch
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> **Special Gene Token Example**
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> In `<|PhenoGemini-Special-Token-Entrez-ID-64087|>`, the numeric value after the final hyphen represents the Entrez Gene ID.
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#
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For questions about individual modules or accessing additional data, please email `dr.wunan@pumch.cn`, `jeffchenmed@gmail.com`, or `caijh09@gmail.com`.
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extra_gated_fields:
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I agree to use this model for non-commercial use ONLY: checkbox
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---
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# Overview
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This model ranks candidate disease-causing genes based on a patient’s phenotypic information. During inference, it does not generate a full free-text response. Instead, it performs gene-token subspace ranking on the logits at the final position and outputs a prioritized list of genes.
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> **Visit https://github.com/discostudy/phenogemini
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> for additional usage examples and demonstration data derived from real-world cohorts.**
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# Step 1: Generate Prompt
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Use `https://phenogemini.org` to generate a prompt that includes similar patients.
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# Step 2: Inference
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```python
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from transformers import AutoModelForCausalLM, AutoTokenizer
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import torch
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> **Special Gene Token Example**
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> In `<|PhenoGemini-Special-Token-Entrez-ID-64087|>`, the numeric value after the final hyphen represents the Entrez Gene ID.
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# Contact
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For questions about individual modules or accessing additional data, please email `dr.wunan@pumch.cn`, `jeffchenmed@gmail.com`, or `caijh09@gmail.com`.
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