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1. ZigZagLLMs ZigZagLLMs Public

   Persistent Topological Features in Large Language Models

   Jupyter Notebook 19 3

2. PLM4Muts PLM4Muts Public

   Python 9

3. MSARC MSARC Public

   Code for clustering MSA representations to drive AF2 predictions toward alternative states.

   Jupyter Notebook 8 2

4. token_geometry token_geometry Public

   Geometry of Tokens in Internal Representations of Large Language Models

   Jupyter Notebook 7 2

5. ESM3-PPISites ESM3-PPISites Public

   Protein Protein Interaction Sites Prediction - ESM3-PPISites

   HTML 6

6. TopoFisher TopoFisher Public

   Differentiable persistent-homology pipelines for learning simulation-based inference summaries by maximizing local Gaussian Fisher information. Includes experiments on spirals, Gaussian random fiel…

   Python 3