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.

Articles

A Guide to Designing New Functional Proteins and Improving Protein Function, Stability, and Diversity with Generative AI

Jul 2

• 36

RFDiffusion Potentials

May 14

• 14

Predicting the Effects of Mutations on Protein Function with ESM-2

Dec 13, 2023

• 6

Faster Persistent Homology Alignment and Protein Complex Clustering with ESM-2 and Persistence Landscapes

Nov 30, 2023

• 1

Clustering Protein Complexes using Persistent Homology and Finetuning ESM-2 for PPI Network Prediction

Nov 29, 2023

ESM-2 for Generating and Optimizing Peptide Binders for Target Proteins

Nov 23, 2023

• 3

Persistent Homology Alignment (PHA): Replacing Multiple Sequence Alignments using ESM-2 and Persistent Homology

Nov 15, 2023

Predicting Protein-Protein Interactions Using a Protein Language Model and Linear Sum Assignment

Oct 15, 2023

• 7

ESMBind (ESMB) Ensemble Models

Sep 22, 2023

• 4

ESMBind (ESMB): Low Rank Adaptation of ESM-2 for Protein Binding Site Prediction

Sep 15, 2023

• 13

Organizations

AmelieSchreiber's activity

New activity in microsoft/Graphormer 17 days ago

Protein-Ligand Dataset Missing

#1 opened 17 days ago by

AmelieSchreiber

New activity in hpcai-tech/open-sora 2 months ago

Update README.md

#7 opened 2 months ago by

AmelieSchreiber

New activity in chao1224/MoleculeSTM 7 months ago

Inference Code Examples

#1 opened 7 months ago by

AmelieSchreiber

New activity in GleghornLab/SYNTERACT 9 months ago

Random train/test split?

#3 opened 9 months ago by

AmelieSchreiber

New activity in AmelieSchreiber/phi_1_5_vicgalle_alpaca-gpt4 11 months ago

Upload model

#1 opened 11 months ago by

AmelieSchreiber

New activity in colbyford/evodiff 11 months ago

Functional Motif Scaffolding and Binder Design Support

#1 opened 11 months ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp1 12 months ago

Librarian Bot: Add base_model information to model

#1 opened about 1 year ago by

librarian-bot

New activity in AmelieSchreiber/esm2_t6_8M_general_binding_sites_v2 about 1 year ago

Adding `safetensors` variant of this model

#4 opened about 1 year ago by

AmelieSchreiber

New activity in wwydmanski/esmfold about 1 year ago

ESM-IF1 space?

#4 opened about 1 year ago by

AmelieSchreiber

New activity in osanseviero/esmfold about 1 year ago

Could you restart this space

#6 opened about 1 year ago by

AmelieSchreiber

New activity in wwydmanski/esmfold about 1 year ago

Batch Folding?

#3 opened about 1 year ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t6_8M_UR50D-finetuned-secondary-structure about 1 year ago

Adding `safetensors` variant of this model

#1 opened about 1 year ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t6_8M_UR50D-finetuned-localization about 1 year ago

Adding `safetensors` variant of this model

#1 opened about 1 year ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t6_8M_UR50D_rna_binding_site_predictor about 1 year ago

Adding `safetensors` variant of this model

#1 opened about 1 year ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t6_8M_UR50D_sequence_classifier_v1 about 1 year ago

Adding `safetensors` variant of this model

#2 opened about 1 year ago by

AmelieSchreiber

New activity in yiminghuang47/esm2_t33_650M_UR50D-finetuned-MHC about 1 year ago

Using the model

#1 opened about 1 year ago by

AmelieSchreiber

New activity in merle/PROTEIN_GENERATOR about 1 year ago

Hello from Joseph Grace (Sydney) and congratulations on your fabulous protein generator.

#4 opened about 1 year ago by

DrGrace

New activity in facebook/esm2_t6_8M_UR50D about 1 year ago

PEFT LoRA and QLoRA

#10 opened about 1 year ago by

AmelieSchreiber

Amelie Schreiber

AI & ML interests

Articles

A Guide to Designing New Functional Proteins and Improving Protein Function, Stability, and Diversity with Generative AI

RFDiffusion Potentials

Predicting the Effects of Mutations on Protein Function with ESM-2

Faster Persistent Homology Alignment and Protein Complex Clustering with ESM-2 and Persistence Landscapes

Clustering Protein Complexes using Persistent Homology and Finetuning ESM-2 for PPI Network Prediction

ESM-2 for Generating and Optimizing Peptide Binders for Target Proteins

Persistent Homology Alignment (PHA): Replacing Multiple Sequence Alignments using ESM-2 and Persistent Homology

In Silico Directed Evolution of Protein Sequences with ESM-2 and EvoProtGrad

QLoRA for ESM-2 and Post Translational Modification Site Prediction

Estimating the Intrinsic Dimension of Protein Sequence Embeddings using ESM-2

Predicting Protein-Protein Interactions Using a Protein Language Model and Linear Sum Assignment

ESMBind (ESMB) Ensemble Models

ESMBind (ESMB): Low Rank Adaptation of ESM-2 for Protein Binding Site Prediction

Organizations

AmelieSchreiber's activity

Protein-Ligand Dataset Missing

Update README.md

Inference Code Examples

Random train/test split?

Upload model

Functional Motif Scaffolding and Binder Design Support

Librarian Bot: Add base_model information to model

Adding `safetensors` variant of this model

ESM-IF1 space?

Could you restart this space

Batch Folding?

Adding `safetensors` variant of this model

Adding `safetensors` variant of this model

Adding `safetensors` variant of this model

Adding `safetensors` variant of this model

Using the model

Hello from Joseph Grace (Sydney) and congratulations on your fabulous protein generator.

PEFT LoRA and QLoRA