ProtFlash: A lightweight protein language model
bioinformatics pretrained-models protein-sequence protein-representation-learning protein-embeddings protein-language-model
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Mar 1, 2026 - Python
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protein-embeddings
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Transmembrane proteins predicted through Language Model embeddings
machine-learning bioinformatics deep-learning pytorch protein-prediction transmembrane-proteins protein-embeddings
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Feb 24, 2026 - Python
Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.
visualization webgl machine-learning bioinformatics protein-structure computational-biology embeddings dimensionality-reduction proteomics umap alphafold protein-embeddings protein-language-models annotation-transfer
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Sep 6, 2026 - TypeScript
JAX/Flax port of AbLang2's AbRep encoder: differentiable antibody language-model embeddings and per-block attention, loading the original weights unchanged.
machine-learning bioinformatics deep-learning computational-biology transformer drug-discovery flax antibody immunoinformatics jax protein-embeddings protein-language-model antibody-design ablang ablang2
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Aug 21, 2026 - Python
Repository containing bio_embeddings resources
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Jan 2, 2021
Similarity search for protein sequences using ESM-2 embeddings and Approximate Nearest Neighbor (ANN) methods.
bioinformatics blast twilight-zone protein-embeddings remote-homology-detection esm2 protein-similarity
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Feb 25, 2026 - Python
A workspace for computational biology — built solo, in public, under MIT.
python open-source bioinformatics nextjs protein-structure computational-biology three-js protein-embeddings
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May 31, 2026 - TypeScript
Transmembrane proteins predicted through Language Model embeddings
machine-learning bioinformatics deep-learning pytorch protein-prediction transmembrane-proteins protein-embeddings
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Jun 12, 2022
Protein homology search using transformer-based embeddings and Approximate Nearest Neighbor methods for efficient biological similarity detection
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Apr 17, 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
LLM-powered classification of phage protein functions to identify strong lytic candidates against Klebsiella, using transfer learning and biological embeddings.
hackathon transfer-learning phage antimicrobial-resistance protein-classification klebsiella protein-embeddings bacteriophage esm-model phagos
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May 22, 2025 - Jupyter Notebook
This work was aimed at finding methods to identify the most distant proteins and most diverse subsets of proteins from large protein databases in a scalable and efficient way using a dataset of protein embeddings from SwissProt, data mining techniques and metaheuristics.
data-science bioinformatics proteins machine-learning-algorithms bigdata bruteforce embeddings memetic-algorithms tabu-search diversity-measures dissertation-project metaheuristic-algorithms protein-embeddings maxsum
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Jan 10, 2024 - Python
Extract sequence embeddings from ESM protein language models with minimal setup.
esm esmc protein-embeddings embeddings-extraction protein-language-model protein-sequence-embeddings esm2 sequence-representation
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May 31, 2026 - Python
Unsupervised clustering of human kinases using ESM-2 protein language model embeddings and sequence features
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Apr 2, 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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Sep 2, 2026 - TypeScript
Embedding-space analysis of VH antibody diversity across human, mouse, and rat — ESM2 vs AntiBERTy, pooling strategy vs CDR masking, with paired bootstrap statistics.
machine-learning bioinformatics computational-biology representation-learning antibody-sequences protein-embeddings esm2 antiberty
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Apr 26, 2026 - Shell
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Mar 16, 2026 - Python
Quantum-informed IBD modeling using ESM protein embeddings and Qiskit QSVC/quantum kernels; CLI for ingest → train → report.
machine-learning genomics computational-biology ibd reproducibility esm qiskit protein-embeddings quantum-kernel qsvc
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Aug 10, 2026 - Python
Benchmarking 1st and 2nd generation protein language model embeddings (ESM-C, Ankh2) on global and local protein property prediction using the ATLAS dataset.
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Jun 23, 2026 - Python
Protein sequence embedding visualizer across transformer layers — layer-wise PCA projections with amino acid tracking
visualization bioinformatics transformers pytorch pca research-software protein-embeddings protein-language-models
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Jul 12, 2026 - Python
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