Aplications of sliding sampling to biological sequences.

Preprint first version

https://www.researchsquare.com/article/rs-1691291/v1

Blog posts

https://tavoglc.medium.com/list/machine-learning-and-covid19-0659a2c0bb92

Datasets

Selected sequences

https://www.kaggle.com/datasets/tavoglc/covid19-sequences-fasta

Kmer frequencies

https://www.kaggle.com/datasets/tavoglc/covid19-sequences-extended

Adjacency matrix model 3

https://www.kaggle.com/datasets/tavoglc/covid19-graph-sequences

Adjacency matrix model 4

https://www.kaggle.com/datasets/tavoglc/covid19-bidirectional-graphs

Adjacency matrix model 5 and model 6

https://www.kaggle.com/datasets/tavoglc/covid19-graphs-by-fragments

Meta data

https://www.kaggle.com/datasets/tavoglc/covid19-metadata

Weather data

https://www.kaggle.com/datasets/tavoglc/weather-data-in-2021

American continent data

https://www.kaggle.com/datasets/tavoglc/covid19-in-the-american-continent

Europe data

https://www.kaggle.com/datasets/tavoglc/covid19-cases

Weather data 2

https://www.kaggle.com/datasets/tavoglc/covid19-cases

Notebooks

Model 1

Original Architecture Tensorflow https://www.kaggle.com/code/tavoglc/seasonal-disentangling-of-sars-cov-2

Improved Model JAX https://www.kaggle.com/code/tavoglc/autoencoders-jax-and-sars-cov2

Model 2

https://www.kaggle.com/code/tavoglc/patterns-inside-sars-cov-2-sequences

Model 3

https://www.kaggle.com/code/tavoglc/convolutional-vae-for-sars-cov-2 https://www.kaggle.com/code/tavoglc/covid-19-sequence-disentangling-with-kl-annealing Its the original architecturer, it was reduced due to large training times, equal to the model 4 architecture.

Model 4

https://www.kaggle.com/code/tavoglc/bidirectional-encoding-of-sars-cov-2-sequences

Model 5 and 6

https://www.kaggle.com/code/tavoglc/fragment-based-encoding-of-sars-cov2

Dynamical model

https://www.kaggle.com/code/tavoglc/sars-cov2-dynamical-vae-modeling

Other analysis

Composition paths

https://www.kaggle.com/code/tavoglc/temporal-paths-inside-sars-cov2

Pandemic peaks and day length

https://www.kaggle.com/code/tavoglc/worldwide-covid-19-peak-prediction

Time scales

https://www.kaggle.com/code/tavoglc/covid-19-pandemic-under-different-time-scales

Genetic mimicry

https://www.kaggle.com/code/tavoglc/measuring-similarity-between-sars-co2-and-the-host

Pangolin classification model

https://www.kaggle.com/code/tavoglc/sarscov2-variant-classification-model

Time series analisis

https://www.kaggle.com/code/tavoglc/seasonal-and-trend-components-in-sars-cov2

Pandemic synchronization

https://www.kaggle.com/code/tavoglc/fractional-calculus-and-the-covid19-pandemic