Experience
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
- create a programming system that can simulate the embryo morphology, mainly shape, based on history description of cells development
- find a way to compare embryos both at a cell level and at a level of the whole embryo
- Results:
- selected a previously developed spherical weighted voronoi diagram as a basic model to present embryo shape, ported to python language the optimization software that extracts voronoi parameters from embryo images
- added a peanut-shape cells processing and improved optimization parameters initialization for more accurate spherical weighted voronoi diagram construction
- presented the evolution of voronoi parameters during the development process and for different embryos as multidimensional trajectories in space, processed them with space reduction techniques, and compared results for different embryos
- using transtab software created a neural network to predict cells parameters and division probability for the next step based on the recent development history of cell and its neighbors, the analysis of results reveals that further investigation and system improvements are required
- compared shape of cells with iterative closest point and field level set approaches and their modifications, the results indicated that cells similarity notion has to be determined in the context of the considered problem
- skills:
- Computational biology, Morphology, Voronoi diagrams, Image processing, Machine learning, Graph databases
- technologies:
- Python, PyCharm, NumPy, SciPy, Matplotlib, Transtab, Neo4j, Cypher
May 2017 - September 2021: PhD student, Research engineer, INRIA, University of Strasbourg, Strasbourg, France
- Objectives:
- find the best estimation approach for the liver’s boundary conditions to improve the simulation accuracy in an augmented reality system created for surgery
- investigate biomechanical models to simulate a realistic liver behavior and influence of boundary conditions in real time
- find a solution to compute statistical approximation for liver attachments based on available data
- Results:
- selected a hyperelastic finite element method with Saint Venant-Kirchhoff material for liver deformations and cubic spring system for boundary conditions
- implemented an approach based on reduced-order unscented Kalman filtering as the best choice for real-time performance/accuracy trade off
- participated in software module implementation that allows estimating various model parameters using nonlinear Kalman filters
- developed an approach using large deformation diffeomorphic metric mapping to obtain statistics for ligament positions
- performed experiments based on synthetic and real data to show the improvement in accuracy for simulations with estimated boundary conditions
- skills:
- Augmented reality, Numerical simulation, Finite element method, Kalman filters, Diffeomorphic metric mapping
- technologies:
- OpenCV, PCL, C++, Python, SOFA, FEBio, QtCreator
May 2014 - November 2016: Software and research engineer, Scientific-Production Affiliate Energiya, Factory Energiya, Saint Petersburg, Russia
- Objectives:
- participate in module writing and testing to find noise-like signals in the radio waves spectrum, collect statistics about characteristics of signals from different satellites using a signal analyzing software
- participate in software development to manage data recordings from the antenna, signal detection and database processing for detected elements in records
- participate in software development for clustering and classification of obtained signals from raw input data
- Results:
- implemented a software module that analyzes noise-like signal appearance and collects their basic information
- employed a module that searches frequency-hopping spread spectrum signals and extracts their basic parameters
- considered different clusterization methods, implemented a prototype to process the data based on mixture models
- skills:
- Digital signal processing, Fourier analysis
- technologies:
- C++, MATLAB, Qt, IPP, Visual Studio
August 2010 - February 2014: Software engineer, OOO Bodynova, Saint Petersburg, Russia
- Objectives:
- participate in developing server-client software complex to model a patient body shape and results of surgical procedures
- investigate available physically based modeling methods and biomechanical properties of skin, adipose, muscles, and bones
- develop a new physically based approach to model the result of an implant or expander placement under soft tissues, estimate simulation results accuracy and calculation time for the developed method
- Results:
- employed software that simulates implant placement under soft tissues
- developed the multilayer nonlinear mass-spring system to describe soft tissues deformation
- implemented the modification of a voxel model to accelerate the processing of collision between implants and soft tissues
- skills:
- Virtual reality, Numerical simulation, Mass-spring system, 3D computer graphics
- technologies:
- C++, Wolfram Mathematica, Wild Magic, Visual Studio
July 2008 - July 2010: Intern, Associate software engineer, EMC corporation, Saint Petersburg, Russia
- Objectives:
- participate in a new storage system development
- verify code with Linux-based open-source utilities
- configure hardware of storage systems for remote access possibility
- Results:
- contributed to the code that writes data directly to disk, without using random access memory
- contributed to the module responsible for cache data saving in case of emergency shut off
- skills:
- Storage device drivers, Linux development
- technologies:
- C, Perl