A PyTorch Basecaller for Oxford Nanopore Reads

Applied Computational Genomics Course at UU: Spring 2020

The DPA package is the scikit-learn compatible implementation of the Density Peaks Advanced clustering algorithm. The algorithm provides robust and visual information about the clusters, their stat…

Analyses performed for the nanocompore paper

Open source code for AlphaFold.

A resource for learning about ML, DL, PyTorch and TensorFlow. Feedback always appreciated :)

🤗Transformers: State-of-the-art Natural Language Processing for Pytorch and TensorFlow 2.0.

Jupyter Notebook tutorials on solving real-world problems with Machine Learning & Deep Learning using PyTorch. Topics: Face detection with Detectron 2, Time Series anomaly detection with LSTM Autoe…

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

Deep Learning (with PyTorch)

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Implementation of various self-attention mechanisms focused on computer vision. Ongoing repository.

MiniFold: Deep Learning for Protein Structure Prediction inspired by DeepMind AlphaFold algorithm

Tutorials on implementing a few sequence-to-sequence (seq2seq) models with PyTorch and TorchText.

Protein sequence classification with self-supervised pretraining

Scripts and modules for training and testing neural network for ECG automatic classification. Companion code to the paper "Automatic diagnosis of the 12-lead ECG using a deep neural network".

This is the second part of the Deep Learning Course for the Master in High-Performance Computing (SISSA/ICTP).)

Public repository associated with "Deep Learning for ECG Analysis: Benchmarks and Insights from PTB-XL"

Predicting protein structure through sequence modeling

A list of deep learning implementations in biology

Advanced Deep Learning Lectures for the Master in HPC (SISSA/ICTP, Trieste)