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AmelieSchreiber 
posted an update 3 months ago
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2422
Latest OpenAI Parameter Golf Competition Training Run BPB (<1K steps on a single 4090) See: ToricBLM, ToricGT, and TropicalGT methods
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AmelieSchreiber 
posted an update 4 months ago
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192
In algebraic geometry, embedding tropical varieties into toric varieties relies on the process of tropicalization and the use of toroidal embeddings. Rather than embedding as geometric spaces, tropical varieties are embedded as polyhedral fans or cone complexes within the fans of target toric varieties to study compactifications and intersection theory.

Toric Varieties: Geometric varieties constructed from combinatorial data known as fans (collections of polyhedral cones). Tropicalization: A procedure that maps an algebraic variety X (typically a subvariety of an algebraic torus T) to a polyhedral complex in a real vector space via valuations. Toric Closures: When you embed a tropical variety in a compact toric variety, the boundary points correspond to limits of points in the variety going towards the boundary of the torus. Embedding Methodologies...Toric Compactification: Any tropical variety (a rational polyhedral fan) can be compactified by embedding it into a complete toric variety. The fan of the toric variety is chosen to contain the tropical variety as a subcomplex, which encodes the combinatorics of the compactification. Toroidal Embeddings: For varieties that are not strict toric varieties, they can often be mapped into toric varieties using the theory of toroidal embeddings. This involves equipping the tropicalized spaces (cone complexes) with balancing conditions and intersection theories.
AmelieSchreiber 
posted an update 4 months ago
AmelieSchreiber 
posted an update over 2 years ago
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6093
A list of my favorite articles I've written on Hugging Face (the others are kind of mid imo):
https://huggingface.co/blog/AmelieSchreiber/a-new-era-of-enzyme-engineering

https://huggingface.co/blog/AmelieSchreiber/protein-optimization-and-design

https://huggingface.co/blog/AmelieSchreiber/rfdiffusion-potentials

https://huggingface.co/blog/AmelieSchreiber/mutation-scoring

https://huggingface.co/blog/AmelieSchreiber/esmbind

https://huggingface.co/blog/AmelieSchreiber/esm2-ptm

https://huggingface.co/blog/AmelieSchreiber/directed-evolution-with-esm2

https://huggingface.co/blog/AmelieSchreiber/intrinsic-dimension-of-proteins

https://huggingface.co/blog/AmelieSchreiber/plm-persistent-homology-msa-replacement

https://huggingface.co/blog/AmelieSchreiber/faster-pha
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AmelieSchreiber 
posted an update over 2 years ago
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Currently attempting to hack EvoDiff to generate binders for target proteins with some interesting results. The generated binders tend to change conformation, sometimes drastically, when bound to the target proteins compared to their unbound states. Below is the target protein with an IDR linker, the generated binder, and the binder bound to the target protein with the IDR linker structure as predicted by ESMFold. Notice how the binder goes from being a solid alpha-helix, to being beta-sheets (in orange). That's quite a change in tertiary structure!
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