Projects

MetaGraph
A C++ framework library for indexing very large collections of DNA/Protein sequences and a tool for sequence search, alignment, and assembly. Although the target use cases of MetaGraph overlap with BLAST, MetaGraph mainly focuses on the scalable indexing of raw sequencing data in annotated de Bruijn graphs with up to $\sim 10^{12}$ nodes and $\sim 10^{7}$ annotation labels. It also provides an online platform MetaGraph Online.
Compressed Hybrid Bit Vector Representations
Hybrid schemes for representing bit vectors in compressed space.
GeoDNA
A portal for DNA sequence search and geographical positioning based on the metagenomic MetaSUB data.
The initial prototype was set up on a weekend but it served well and was used as a base for the MetaGraph Search platform. Other contributors: Marc Zimmermann and Jiayu Chen.
De Bruijn Graph Visualizer
A small web app visualizing de Bruijn graphs and the BOSS table. It was written for educational purposes to interactively illustrate the core data structure used for graph representation in MetaGraph.
Protein Scoring
A method for single-model coarse-grained protein quality assessment developed during my internship at Inria Grenoble-Rhône-Alpes.
Sentiment Analysis
A small demo for sentiment analysis of reviews on Russian banks (one of those quick hands-on projects I did when studied at YSDA).
After a night of “bombarding” banki.ru with random requests for web scraping, our dorm network was banned by IP. Fortunately, 5k successfully scraped reviews were enough to complete the project, which I was reminded about each time my roommates or I had to use a VPN for accessing the website to check reviews on banks since then.
Activity Prediction
Classification of time-series data from smartphone accelerometer sensor. Implemented as a practical demonstration of the methods developed in my Bachelor’s thesis.