Code for processing FASTA files into batched, tokenized, and padded sequences, and training FlashAttention-based implementations of ESM-2
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Dec 23, 2025 - Python
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esm-2
Here are 10 public repositories matching this topic...
Biosecurity retrieval compendium — ESM-2 homology cliff analysis, 5 papers, 4 pre-registrations, 9360 per-cell results, SHA-256 manifest
reproducibility homology pre-registration reproducibility-challenge biosecurity esm-2 homology-protein-modelling reproducibility-research
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May 12, 2026 - Python
graph-convolutional-network graph-attention-network protein-language-model esm-1b esm-2 kolmogorov-arnold-networks esm-3 binding-sites-prediction
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Apr 19, 2026 - Jupyter Notebook
This paper has been published on Interdisciplinary Sciences: Computational Life Sciences.
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Mar 31, 2025 - Python
A Graph Neural Network (Siamese GATv2) pipeline using ESM-2 embeddings to map the Dengue NS1–Human interactome. Discovered a novel link between NS1 and Carbonic Anhydrases.
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Feb 23, 2026 - Jupyter Notebook
Graph-based Protein-Peptide Interaction Predictor. Reranking candidates using ESM-2 embeddings and Graph Neural Networks (GNN) on PROPEDIA data.
structural-biology drug-discovery 3dmol pytorch-geometric gnn bioin protein-peptide esm-2 apple-mlx propedia
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Mar 30, 2026 - Python
A hybrid C++/Python pipeline for remote protein homology detection, coupling ESM-2 language model embeddings with custom Neural-LSH for scalable approximate nearest neighbor search.
python machine-learning bioinformatics cpp computational-biology lsh nearest-neighbor-search protein-embeddings remote-homology-detection protein-language-models esm-2 neural-lsh
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Jan 30, 2026 - Python
Bioinformatics capstone of the UoA DI 'Software Development for Algorithmic Problems' trilogy. Protein remote-homolog search on SwissProt-50k via ESM-2 embeddings + 6 ANN methods (brute, LSH, Hypercube, IVF-Flat, IVF-PQ, Neural LSH), benchmarked against BLAST.
bioinformatics university-project nearest-neighbor-search blast swissprot protein-search homolog-detection approximate-nearest-neighbor esm-2 neural-lsh
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May 10, 2026 - Python
ProteinFlex is a comprehensive platform for protein structure analysis and drug discovery, leveraging advanced AI and machine learning techniques. The platform combines state-of-the-art protein structure prediction with interactive visualization and sophisticated drug discovery tools.
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Apr 23, 2025 - Python
Empirical dual-use risk assessment of protein language models (ESM-2) and structure-based design tools (ProteinMPNN)
evaluation ai-safety biosecurity protein-language-model foundation-models biosafety evodiff esm-2 dual-use proteinmpnn ligandmpnn
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May 14, 2026 - Python
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