duolinwang / acm-bcb-2019-tutorial

Slides, code, and examples for the Low-dimensional Representation of Biological Sequence Data tutorial at the ACM-BCB 2019 conference

ACM-BCB-2019-Tutorial

Slides, code, and examples for the Low-dimensional Representation of Biological Sequence Data tutorial at the ACM-BCB 2019 conference. These materials have been partially funded by the NSF ISS BIGDATA grant No. 1836914.

• ACM-BCB-2019_embedding_tutorial: slides for the Low-dimensional Representation of Biological Sequence Data tutorial at the ACM-BCB 2019 conference.
• word2vec-examples.ipynb: a Jupyter notebook with two simple examples using Word2Vec in the context of english words and biological sequence data. Requires sequences.txt, questions-words.txt, and a pretrained Word2Vec embedding (e.g. https://drive.google.com/file/d/0B7XkCwpI5KDYNlNUTTlSS21pQmM/edit).
• multilateration-examples.ipynb: a Jupyter notebook with two examples using multilateration to generate embeddings for DNA 3-mers and to generate and embedding for the Hamming graph over amino acid sequences of length 8. Requires multilateration.py.
• multilateration.py: code implementing the Information Content Heuristic (ICH) algorithm for approximating the metric dimension of graphs.
• questions-words.txt: analogies for testing Word2Vec embeddings (from https://github.com/nicholas-leonard/word2vec/blob/master/questions-words.txt).
• human_cds.txt: human coding sequences obtained from Ensembl Biomart 8/13/2019 (https://www.ensembl.org/biomart/martview/) Human genes (GRCh38.p12).
• sequences.txt: each sequence from humans_cds.txt on a separate line.
• parseData.py: generate sequences.txt given human_cds.txt.
• .loc files: Word2Vec embeddings based on sequences.txt using different dimensions and reading frames.
• Multilateration
  • Code to generate resolving sets for Hamming graphs.
  • Embeddings of Hamming graphs and codons generated using multilateration.
• Word2Vec
  • Code to generate embeddings of k-mers based on the data in sequences.txt.
  • Embeddings of k-mers using Word2Vec
  • An NLP example of Word2Vec.
• TSNE
  • Code to visualize embeddings using t-SNE.