Here is the description of my past working experience:

April 2022 - November 2023: Postdoctoral researcher in computational biology, University of Montpellier, Montpellier, France

  • Objectives:
    • better understand how a single cell (fertilized egg) can develop into a complex biological organism
    • simulate embryo morphology, mainly shape, based on available embryo data and historical description of cells development
  • Results:
    • represented embryo cells shape as parameters of a spherical weighted Voronoi diagram; ported from MATLAB to Python an optimization module, which extracts diagram parameters from available images, to execute the computation without license restrictions on the Jean Zay supercomputer
    • added peanut-shape cells processing and improved initialization of optimization parameters to construct the spherical weighted Voronoi diagram more accurately
    • implemented a software system to process and store in a Neo4j graph database the computed diagrams parameters and biological markers of cells
    • described the evolution of Voronoi diagram parameters during the development process and for different embryos as multidimensional trajectories in space
    • created a neural network using Transtab software to predict the dynamics of cells shape together with their division probability from a development history of the cells and constructed trajectories, the results show a possibility to predict the probability of cell division with an accuracy of 82%
  • skills:
    • Computational biology, Morphology, Voronoi diagrams, Image processing, Machine learning, Graph databases
  • technologies:
    • Python, NumPy, SciPy, Scikit-image, Matplotlib, Miniconda, Pandas, TensorFlow, Transtab, PyCharm, MATLAB, Neo4j, Cypher, Ubuntu Linux, Bash, Git

May 2017 - September 2021: PhD student, Research engineer, INRIA, University of Strasbourg, Strasbourg, France

  • Objectives:
    • estimate liver’s boundary conditions to improve the simulation accuracy in an augmented reality system created for the surgery
    • simulate a realistic liver behavior as well as an influence of the surrounding organs and tissues in real time
  • Results:
    • constructed a hyperelastic finite element method for liver deformations and a cubic spring system for boundary conditions
    • developed a component describing springs with polynomial stress strain relation, which was integrated into SOFA framework
    • participated in a software module implementation that allows estimating various model parameters using nonlinear Kalman filters
    • employed an approach based on a reduced-order unscented Kalman filter as the best choice for real-time performance/accuracy trade off
    • segmented and extracted markers from RGB-D image sequence to obtain observations for estimation process
    • carried out an optimization based on a preconditioner to improve the performance of the estimation process (computation time is 26% less)
    • created an approach based on deformable registration of liver shapes (large deformation diffeomorphic metric mapping) to obtain statistics for ligament positions
    • performed experiments based on synthetic (error is 66% less) and real (error is 23% less) data to show the improvement in accuracy for simulations with estimated boundary conditions
  • skills:
    • Augmented reality, Numerical simulation, Finite element method, Mass-spring system, Kalman filters, Diffeomorphic metric mapping
  • technologies:
    • C++, STL, Eigen, OpenCV, PCL, SOFA, FEBio, Qt, CMake, QtCreator, Python, NumPy, Matplotlib, Deformetrica, Ubuntu Linux, Bash, Git

May 2014 - November 2016: Software and research engineer, Scientific-Production Affiliate Energiya, Factory Energiya, Saint Petersburg, Russia

  • Objectives:
    • create modules to find various signals in the radio waves spectrum, maintain a database to store the elements detected in records, collect statistics about characteristics of signals with an analyzing tool
  • Results:
    • employed a software module that analyzes noise-like signal appearance and collects their basic information
    • ported from MATLAB to C++ a module that searches for frequency-hopping spread spectrum signals and extracts their basic parameters
    • created a component that puts information about detected signals and their parameters to a PostgreSQL database
    • developed a graphical user interface to show the spectrum frequency/sweep and indicate signals location
  • skills:
    • Digital signal processing, Fourier analysis, FFT
  • technologies:
    • C++, Intel IPP, STL, Boost, Qt, CMake, Visual Studio, SQL, PostgreSQL, MATLAB, MS Windows, Git

August 2010 - February 2014: Software engineer, OOO Bodynova, Saint Petersburg, Russia

  • Objectives:
    • create a server-client software complex to model a patient body shape and results of implant and expander surgery procedures
    • simulate the biomechanical properties of skin, adipose, muscles, bones, and implants realistically
  • Results:
    • developed software that simulates implant placement under soft tissues, estimated its accuracy and computation time
    • created a graphical user interface for the simulation software that allows selecting an implant from a catalogue and choosing its placement parameters
    • constructed an innovative multilayer, nonlinear, and anisotropic mass-spring system to describe soft tissues deformation, implemented as a C++ software unit
    • carried out an OpenGL based rendering component to observe a mass-spring system behavior
    • proposed and employed a modification of a voxel model to accelerate the processing of collision between implants and soft tissues
  • skills:
    • Virtual reality, Numerical simulation, Mass-spring system, Image processing, Computational geometry, 3D computer graphics
  • technologies:
    • C++, STL, WildMagic, WxWidgets, OpenCV, Bullet physics engine, OpenGL, OGRE, Visual Studio, HTML/CSS, JavaScript, Wolfram Mathematica, MS Windows, SVN

July 2008 - July 2010: Intern, Associate software engineer, EMC corporation, Saint Petersburg, Russia

  • Objectives:
    • participate in a new storage system (driver) development
  • Results:
    • developed low-level driver components for the data storage system, including a direct access disk mechanism (Bypass I/O) and a module for saving data cache in case of emergency shut off
    • configured hardware of four storage systems for remote access connections
  • skills:
    • Storage device drivers, Linux development
  • technologies:
    • C, gdb, make, Valgrind, Linux utils, Vim, Perl, Linux, SVN

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