AmelieSchreiber/BioKinema-bucket
4.16 GB
Amelie Schreiber
AmelieSchreiber
AI & ML interests
Diffusion and flow matching models for proteins, small molecules, DNA, and RNA, protein language models, machine translation, equivariant attention mechanisms, LoRA, and QLoRA.
Recent Activity
updated a bucket 2 days ago
AmelieSchreiber/BioKinema-bucket published a bucket 2 days ago
AmelieSchreiber/BioKinema-bucket published a dataset 3 days ago
AmelieSchreiber/iska-net-2_baseOrganizations
Posts 2
Post
6063
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
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
Articles 17
Article
3
Tropical Quivers for Modern AI: A Guided Tour of a Research Program
ESMBind (or ESMB) are LoRA finetuned ESM-2 models for predicting general binding sites and active sites of proteins based on sequence alone.
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AmelieSchreiber/esm2_t12_35M_lora_binding_sites_770K_v1
Updated • 6 -
AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp3
Token Classification • Updated • 21 • 6 -
AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp2
Token Classification • Updated • 10 -
AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp1
Token Classification • Updated • 8
ESMBind (or ESMB) are LoRA finetuned ESM-2 models for predicting general binding sites and active sites of proteins based on sequence alone.
-
AmelieSchreiber/esm2_t12_35M_lora_binding_sites_770K_v1
Updated • 6 -
AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp3
Token Classification • Updated • 21 • 6 -
AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp2
Token Classification • Updated • 10 -
AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp1
Token Classification • Updated • 8
QLoRAs for various ESM-2 models for predicting binding sites of protein sequences.
models 58
AmelieSchreiber/UBio-E2Former-LSR
Updated
AmelieSchreiber/LucaOne
Updated • 3
AmelieSchreiber/RoseTTAFold2-PPI
Updated
AmelieSchreiber/AlphaChip
Updated • 2
AmelieSchreiber/IgDiff
Updated
AmelieSchreiber/DiG
Updated
AmelieSchreiber/Graphormer
Updated
AmelieSchreiber/esm_mlmppi_ph50_40K
Updated
AmelieSchreiber/esm_mlmppi_ph50_v3
Fill-Mask • 0.7B • Updated • 10
AmelieSchreiber/esm_mlmppi_ph50
Fill-Mask • 0.7B • Updated • 10
datasets 21
AmelieSchreiber/iska-net-2_base
Updated • 17
AmelieSchreiber/ReactZyme
Viewer • Updated • 258k • 29
AmelieSchreiber/pha_clustered_protein_complexes_40K
Viewer • Updated • 40k • 33
AmelieSchreiber/pha_clustered_protein_complexes_30K
Viewer • Updated • 30k • 31
AmelieSchreiber/pha_clustered_protein_complexes
Viewer • Updated • 10k • 27
AmelieSchreiber/interaction_pairs
Viewer • Updated • 118k • 15
AmelieSchreiber/12M_binding_sites
Updated • 10
AmelieSchreiber/ptm_500K
Updated • 68 • 1
AmelieSchreiber/2600K_binding_sites
Updated • 50
AmelieSchreiber/1111K_binding_sites
Updated • 68