amelie-schreiber Goto Github PK

amelie-schreiber.github.io

anomaly_detection_persistent_homology

Detecting anomalous texts with persistent homology of context vectors computed by individual attention heads in language transformers

attention_persistent_homology

Studying how well the persistent homology of collocations and keyphrases are preserved by various models.

chatgpt

Experiments with ChatGPT

confiboot

Confidence bootstrapping for DiffDock

context_persistent_homology_comparisons

Comparing different models' preservation of persistent homology.

directed_evolution

Protein Design by Machine Learning guided Directed Evolution

emergent_topology_of_ideas_in_vision

A repo for persistent homology analysis of ideas in vision transformers, using the attention mechanism to derive the Jensen-Shannon distance between probability distributions associated to tokens.

esm2_lora_binding_sites

Training a Low Rank Adaptation of the protein language model ESM-2 for RNA binding site predictor

esm2_loras

Trying to train LoRAs for ESM-2

esm2_masked_lm

Various Ideas for Protein Masked LM with ESMFold/ESM-2

evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

evoprotgrad

Directed evolution of proteins in sequence space with gradients

fair

NeurIPS 2023 Spotlight paper: Full atom protein pocket design via iterative refinement

get

(Unofficial) GET for proteins

hebrew_context_persistent_homology

Persistent homology of context vectors computed by individual attention heads in Hebrew language models

lora_models

Some ideas and code for LoRA models (Low Rank Adaptation)

multilingual_persistent_homology

We study the persistent homology of the context vectors computed by individual attention heads in multilingual language models

peft-proteomics

Some PEFT models for PPI prediction and symmetry prediction.

pepmlm

Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling

persistent_homology_of_attention

Persistent homology analysis of individual attention heads in transformer models

persistent_homology_of_entanglement

promptprotein

Code and Data for the paper: Multi-level Protein Structure Pre-training with Prompt Learning [ICLR 2023]

protein-vec

Repository for Protein-Vec, a protein embedding mixture of experts model

protein_mutation_scoring

Some scoring functions for predicting the effects of mutations on protein sequences using ESM-2

proteinchat

quantum_surface_codes

Quantum Surface Codes

sampling_protein_language_models

Using variations on Gibbs sampling for directed evolution

sddiff

Diffusion model for generating small molecules

sense-ppi