bioinformatics deep-learning pytorch gene-ontology uniprot multi-label-classification protein-function esm2
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Aug 30, 2026 - Jupyter Notebook
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esm2
Here are 112 public repositories matching this topic...
NTU final year project: MHC-peptide binding prediction with ESM-2, LoRA and structure GNNs
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Oct 29, 2026 - Python
TCR Epitope Generation Model with Top-K Prediction
machine-learning bioinformatics deep-learning transformer t-cell-receptor encoder-decoder-model cross-attention generative-ai esm2
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Oct 31, 2025 - Jupyter Notebook
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Mar 16, 2026 - Python
ESM2-15B Protein Embeddings
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Aug 9, 2025 - Jupyter Notebook
An AI-powered antimicrobial resistance surveillance system — uses a pretrained protein language model (ESM2) to embed bacterial protein sequences, classifies resistance mechanisms against real CARD database gene families, and flags anomalous sequences that don't match known resistance patterns for surveillance follow-up.
python machine-learning bioinformatics scikit-learn pytorch antimicrobial-resistance fastapi protein-language-model esm2
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Oct 1, 2026 - Python
Protein design pipeline - ProteinMPNN sequence generation + independent ESM-2 rescoring + cross-model consensus report, with pinned-seed provenance
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Sep 29, 2026 - Python
Federated learning framework for protein language models (ESM2) using NVFlare + Flower. Supports multi-GPU simulation, HPC/SLURM deployment, and HuggingFace dataset integration.
machine-learning bioinformatics pytorch flower federated-learning protein-language-model nvflare esm2
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Mar 15, 2026 - Python
GraphSSL-MultiCancer-GFM: Graph Self-Supervised Pretraining on 20 Cancers (TCGA/METABRIC) with ESM-2 Protein LM. Cell Reports Methods (Methods Track) Reproduction Package. FDA Schuirmann-1987 TOST Δ₀=0.002 EQUIVALENT.
bioinformatics tcga pytorch reproducibility graph-neural-networks metabric protein-language-model graph-self-supervised-learning esm2 ppi-network multi-cancer-transcriptomics cell-reports-methods tost-equivalence-testing
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Oct 1, 2026 - TeX
Per-residue ligand-binding site prediction from protein structures using frozen ESM-2 embeddings + an MLP head.
bioinformatics deep-learning computational-biology pytorch protein-binding-site protein-language-model esm2
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Jul 9, 2026 - Jupyter Notebook
Sparse-autoencoder feature circuits in the ESM-2 protein LM: top-k SAEs + causal ablation map features to transmembrane & signal-peptide detection; interactive Cytoscape viewer
bioinformatics cytoscape interpretability sparse-autoencoder ablation protein-language-model mechanistic-interpretability esm2 feature-circuits
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Jun 1, 2026
Classifier-free-guided diffusion for VR-VIII viable AAV capsid generation.
computational-biology pytorch protein-design generative-models protein-engineering aav gene-therapy diffusion-models classifier-free-guidance esm2 capsid-design
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Oct 18, 2026 - Jupyter Notebook
The entire Pfam universe as an on-device inference engine: paste a sequence, get a family, offline. Swift/SwiftUI for iOS, iPadOS, macOS, visionOS and watchOS.
bioinformatics structural-biology pfam protein-families coreml swiftui on-device-ml protein-language-model visionos esm2
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Aug 27, 2026 - Swift
Functional-effect landscapes for single amino-acid substitutions (ProteinGym)
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Oct 28, 2026 - Python
Sparse autoencoders discover monosemantic biological concepts across ESM2-650M layers 6/17/33, with causal validation via activation patching.
bioinformatics sparse-autoencoders interpretability mechanistic-interpretability protein-language-models esm2
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Jul 8, 2026 - Python
Antimicrobial-resistance dashboard for the gut-derived pathogens behind infected pancreatic necrosis. BV-BRC genomes, ESM2 embeddings on a Daytona H100, and Fireworks observations that quote only measured numbers. Research prototype, not for clinical use.
bioinformatics genomics hackathon gpu amr daytona antimicrobial-resistance protein-embeddings llm bv-brc copilotkit esm2 fireworks-ai
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Oct 20, 2026 - TypeScript
Exploring the AMR protein embedding landscape with ESM2 and Ankh. Interactive tool at HuggingFace Spaces.
bioinformatics embeddings amr umap card-database antimicrobial-resistance protein-language-model esm2
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Apr 11, 2026 - HTML
ESM-2 and IA3 parameter-efficient functional peptide classification with a Streamlit inference demo
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Jun 11, 2026 - Python
StruSel: Structurome-wide Selectivity of pathogen-exclusive targets
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Apr 22, 2026 - Jupyter Notebook
Interpretable protein sequence classification and AMR active-site identification using Meta AI's ESM-2 and Attention Pooling.
bioinformatics deep-learning transformers computational-biology pytorch explainable-ai protein-language-models esm2
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Oct 28, 2026 - Python
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