Protein sequence classification with self-supervised pretraining
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Nov 29, 2021 - Python
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protein-classification
Here are 18 public repositories matching this topic...
Exploring Evolution-aware & free protein language models as protein function predictors
benchmark pytorch contact-prediction stability multiple-sequence-alignment protein-annotation function-prediction protein-classification alphafold protein-language-model alphafold2 fitness-prediction zero-shot-prediction msa-construction msa-transformer esm1b remote-homology-detection metal-ion-binding
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Sep 28, 2024 - Python
Deep Critical Learning. Implementation of ProSelfLC, IMAE, DM, etc.
deep-learning pytorch image-classification convolutional-neural-networks protein-design protein-function-prediction protein-localization protein-classification bert-transformer protein-transformer
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Dec 23, 2022 - Python
A multi-stage graph neural network classification pipeline for protein meshes.
community-detection 3d-geometry curriculum-learning graph-attention-networks graph-neural-networks protein-classification
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Oct 20, 2025 - Python
Antimicrobial Peptide Scanner Version 2. Open source GLPv3 release of code from 2018 paper "Deep learning improves antimicrobial peptide recognition" published in the journal Bioinformatics: https://doi.org/10.1093/bioinformatics/bty179
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Jan 20, 2025 - Python
Graph Transformer for Protein Structure classification
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Feb 8, 2025 - Python
Pipeline for discovering novel protease inhibtiors at plant pathogen interface.
open-source transformers python3 protein-sequences function-prediction protein-classification colab-notebooks protein-language-model large-language-models protein-language-model-finetuning
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Feb 1, 2026 - Jupyter Notebook
deep-neural-networks deep-learning image-processing regression mnist mnist-classification resnet regression-models cifar10 computervision facial-expression-recognition regression-algorithms cifar-10 mnist-handwriting-recognition binary-classifier cat-vs-dog digit-recognition-mnist protein-classification wine-quality-prediction
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Jul 28, 2020 - Jupyter Notebook
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
TooT-PLM-ionCT: A bioinformatics framework utilizing protein language models for accurate classification of ion channels and ion transporters from membrane proteins.
machine-learning natural-language-processing bioinformatics deep-learning membrane-proteins protein-classification protein-language-models ion-channel-classification ion-transporters
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Nov 1, 2024 - Python
Classify proteins into functional families/domains using pretrained ESM embeddings with interpretable ML (SHAP/LIME), UMAP visualizations, and optional 3D rendering.
machine-learning bioinformatics pytorch esm embedding umap lime protein-family mlflow shap protein-classification
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Dec 7, 2025 - Jupyter Notebook
Personal project dealing on Transformer and Protein family classification
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Oct 29, 2024 - Python
Protein subcellular localization classifier using ESM-2 embeddings and PyTorch MLP.
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Mar 13, 2026 - Jupyter Notebook
Gene Anotation with CNNs
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Apr 9, 2024 - Jupyter Notebook
GNNs for protein graph classification on OGBG-PPA with GCN, GIN and baseline models.
pytorch graph-classification graph-convolutional-network graph-neural-networks pytorch-geometric gnn graph-isomorphism-network protein-classification ogb
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Aug 22, 2025 - Python
A comparative analysis of deep learning algorithms for multi label image classification using microscopic images.
deep-learning image-classification transfer-learning vgg19 fastai rnn-pytorch cnn-pytorch efficientnet protein-classification
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May 9, 2024 - Jupyter Notebook
Assignments Completed during BIO543:Big Data Mining in Healthcare Course in IIITD during Winter 2025 Semester. Professor: Gajendra P.S. Raghava
machine-learning tensorflow sklearn feature-extraction kaggle-competition protein-sequences hyperparameter-tuning iiitd protein-classification cancer-classification bdmh bio543 bdmh-assignments big-data-mining-in-healthcare peptide-classification gene-expression-data
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Apr 29, 2025 - Jupyter Notebook
A machine learning pipeline for eukaryotic signal peptide prediction — from UniProtKB data collection to a CNN-LSTM classifier on ESM-2 embeddings. Implements and benchmarks three methods: a von Heijne PSWM baseline, an SVM with biochemical features, and a deep learning model (F1=0.962, ROC-AUC=0.998).
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Apr 23, 2026 - Jupyter Notebook
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