Amelie-Schreiber
Independent researcher and mathematician, working on protein language models, certain equivariant transformers, Low Rank Adaptations, and QLoRA
Pinned Repositories
anomaly_detection_persistent_homology
Detecting anomalous texts with persistent homology of context vectors computed by individual attention heads in language transformers
confiboot
Confidence bootstrapping for DiffDock
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
hebrew_context_persistent_homology
Persistent homology of context vectors computed by individual attention heads in Hebrew language models
protein_mutation_scoring
Some scoring functions for predicting the effects of mutations on protein sequences using ESM-2
sense-ppi
ShapeMol
Shape conditioned diffusion model for small molecule generation and drug design
transformers_proteins_and_persistent_homology
Transformers, Protein Sequences, and Persistent Homology
Amelie-Schreiber's Repositories
Amelie-Schreiber/esm2_masked_lm
Various Ideas for Protein Masked LM with ESMFold/ESM-2
Amelie-Schreiber/esm2_loras
Trying to train LoRAs for ESM-2
Amelie-Schreiber/esm2_LoRA_binding_sites
Training a Low Rank Adaptation of the protein language model ESM-2 for RNA binding site predictor
Amelie-Schreiber/protein_mutation_scoring
Some scoring functions for predicting the effects of mutations on protein sequences using ESM-2
Amelie-Schreiber/transformers_proteins_and_persistent_homology
Transformers, Protein Sequences, and Persistent Homology
Amelie-Schreiber/ShapeMol
Shape conditioned diffusion model for small molecule generation and drug design
Amelie-Schreiber/confiboot
Confidence bootstrapping for DiffDock
Amelie-Schreiber/sense-ppi
Amelie-Schreiber/study_of_attention
A study of attention from many perspectives
Amelie-Schreiber/anomaly_detection_persistent_homology
Detecting anomalous texts with persistent homology of context vectors computed by individual attention heads in language transformers
Amelie-Schreiber/GET
(Unofficial) GET for proteins
Amelie-Schreiber/sampling_protein_language_models
Using variations on Gibbs sampling for directed evolution
Amelie-Schreiber/hebrew_context_persistent_homology
Persistent homology of context vectors computed by individual attention heads in Hebrew language models
Amelie-Schreiber/Amelie-Schreiber.github.io
Amelie-Schreiber/context_persistent_homology_comparisons
Comparing different models' preservation of persistent homology.
Amelie-Schreiber/Directed_Evolution
Protein Design by Machine Learning guided Directed Evolution
Amelie-Schreiber/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.
Amelie-Schreiber/evodiff
Generation of protein sequences and evolutionary alignments via discrete diffusion models
Amelie-Schreiber/EvoProtGrad
Directed evolution of proteins in sequence space with gradients
Amelie-Schreiber/FAIR
NeurIPS 2023 Spotlight paper: Full atom protein pocket design via iterative refinement
Amelie-Schreiber/multilingual_persistent_homology
We study the persistent homology of the context vectors computed by individual attention heads in multilingual language models
Amelie-Schreiber/peft-proteomics
Some PEFT models for PPI prediction and symmetry prediction.
Amelie-Schreiber/pepmlm
Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling
Amelie-Schreiber/PromptProtein
Code and Data for the paper: Multi-level Protein Structure Pre-training with Prompt Learning [ICLR 2023]
Amelie-Schreiber/protein-vec
Repository for Protein-Vec, a protein embedding mixture of experts model
Amelie-Schreiber/proteinchat
Amelie-Schreiber/SDDiff
Diffusion model for generating small molecules
Amelie-Schreiber/TARDIS
TARDIS: Topological Algorithms for Robust DIscovery of Singularities
Amelie-Schreiber/text_clustering_persistent_homology
Clustering texts using LLMs and persistent homology
Amelie-Schreiber/transformers
🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.