16 10

Amelie Schreiber

AmelieSchreiber

https://mastodon.social/@OctoNoodle

amelie_iska

Amelie-Schreiber

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

RFDiffusion Potentials

1 day ago

• 8

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

2 days ago

• 14

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

Dec 13, 2023

• 2

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

Nov 30, 2023

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

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

• 4

ESMBind (ESMB) Ensemble Models

Sep 22, 2023

• 4

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

Sep 15, 2023

• 5

Organizations

AmelieSchreiber's activity

New activity in chao1224/MoleculeSTM 3 months ago

Inference Code Examples

#1 opened 3 months ago by

AmelieSchreiber

New activity in GleghornLab/SYNTERACT 5 months ago

Random train/test split?

#3 opened 5 months ago by

AmelieSchreiber

New activity in AmelieSchreiber/phi_1_5_vicgalle_alpaca-gpt4 7 months ago

Upload model

#1 opened 7 months ago by

AmelieSchreiber

New activity in colbyford/evodiff 7 months ago

Functional Motif Scaffolding and Binder Design Support

#1 opened 7 months ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp1 8 months ago

Librarian Bot: Add base_model information to model

#1 opened 8 months ago by

librarian-bot

New activity in AmelieSchreiber/esm2_t6_8M_general_binding_sites_v2 8 months ago

Adding `safetensors` variant of this model

#4 opened 8 months ago by

AmelieSchreiber

New activity in wwydmanski/esmfold 9 months ago

ESM-IF1 space?

#4 opened 9 months ago by

AmelieSchreiber

New activity in osanseviero/esmfold 9 months ago

Could you restart this space

#6 opened 9 months ago by

AmelieSchreiber

New activity in wwydmanski/esmfold 9 months ago

Batch Folding?

#3 opened 9 months ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t6_8M_UR50D-finetuned-secondary-structure 9 months ago

Adding `safetensors` variant of this model

#1 opened 9 months ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t6_8M_UR50D-finetuned-localization 9 months ago

Adding `safetensors` variant of this model

#1 opened 9 months ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t6_8M_UR50D_rna_binding_site_predictor 9 months ago

Adding `safetensors` variant of this model

#1 opened 9 months ago by

AmelieSchreiber

New activity in AmelieSchreiber/esm2_t6_8M_UR50D_sequence_classifier_v1 9 months ago

Adding `safetensors` variant of this model

#2 opened 9 months ago by

AmelieSchreiber

New activity in yiminghuang47/esm2_t33_650M_UR50D-finetuned-MHC 9 months ago

Using the model

#1 opened 9 months ago by

AmelieSchreiber

New activity in merle/PROTEIN_GENERATOR 10 months ago

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

#4 opened 10 months ago by

DrGrace

New activity in facebook/esm2_t6_8M_UR50D 10 months ago

PEFT LoRA and QLoRA

#10 opened 10 months ago by

AmelieSchreiber

Amelie Schreiber

AI & ML interests

Articles

RFDiffusion Potentials

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

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

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