Hi, I'm Vladyslav Honcharuk

Researcher in Neurorobotics & Bioinformatics | Data Science Intern at xForest Therapeutics

I enjoy solving complex problems with creative solutions (and a cup of coffee)

View Publications View Research Highlights

About Me

Vladyslav Honcharuk

Hello! I'm Vlad, a researcher passionate about applying computational methods to solve complex problems. Based in Kyoto, Japan, I focus on two main research areas: spatial transcriptomics and eye-tracking data analysis.

As the lead developer of DeepSpaceDB, I've built an easy-to-use interactive spatial transcriptomics database. Additionally, my work in eye-tracking includes developing machine learning systems for schizophrenia detection and analyzing human attention patterns in real-world settings.

When I'm not analyzing data, you'll find me weightlifting, gaming, reading a book or hiking mountains.

Education

Oct 2025 - Apr 2027

Research Student

Kyoto University, Developmental Neurorobotics (Veale) Lab | Kyoto, Japan

Graduate School of Medicine, Department of Neuroscience

Neuroscience research in eye-tracking and behavioral data analysis

MEXT Scholarship recipient

Sep 2020 - Jun 2025

Bachelor's Degree, Computer Science

National Technical University of Ukraine 'Kyiv Polytechnic Institute'

Specialization: Computer Technologies in Biology and Medicine

Thesis: Information System for the Diagnosis of Schizophrenia Using Eye-Tracking Data

Grade: 93/100

Apr 2022 - Sep 2024

Exchange Programs

Kyoto University | Aug 2022 - Sep 2024

Courses: Fundamentals of Artificial Intelligence, Processing and Analyzing Data, Information Networks, Statistics

Akita University | Apr 2022 - Jul 2022

Course: Introduction to Machine Learning

Shibaura Institute of Technology | Apr 2022 - Jul 2022

Courses: Statistical Signal Processing, Bionic and Biomimetic System Engineering, International Development Engineering

Work Experience

Oct 2024 - Present

Data Science Intern

xFOREST Therapeutics | Kyoto, Japan

  • Using RNA 3D structure prediction software for affinity prediction analysis
  • Analyzing RNA-sequencing data
Jan 2024 - Present

Technical Assistant

Kyoto University, Bioinformatics (Vandenbon) Lab | Kyoto, Japan

  • Developing a website for ongoing research in spatial transcriptomics. Orchestrating and analyzing 10x Genomics Visium and Xenium spatial data
  • Using NLP for automated sample metadata extraction from web, using Computer Vision models for H&E image data analysis
  • Contributing to the manuscript writing and presenting research at scientific conferences
Oct 2023 - Present

Research Assistant

Kyoto University, Developmental Neurorobotics (Veale) Lab | Kyoto, Japan

  • Analyzing allocentric and egocentric eye-tracking data
  • Applying machine learning and data analysis techniques to eye-tracking data
  • Presenting my research at scientific conferences through poster presentations
  • Teaching: DP2025: Introduction to Shell-Based Data Processing (Fall 2025) - Teaching Assistant, delivered 3 lectures on Basic Bash and Python

Publications

Papers

2025

DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments

Vladyslav Honcharuk, Afeefa Zainab, Yoshiya Horimoto, Keiko Takemoto, Diego Diez, Shinpei Kawaoka, Alexis Vandenbon

Nucleic Acids Research, 2025

Paper Website

Poster Presentations

2025

DeepSpaceDB 2.0: Benchmarking and standardization of subcellular spatial transcriptomics

Vladyslav Honcharuk, Alexis Vandenbon

NGS EXPO (Nara, Japan), 2025

LiMe retreat (Awaji, Japan), 2025

Poster
2025

Automated Schizophrenia Detection Through Video-Based Eye Movement Feature Analysis (My Bachelor's thesis project)

Vladyslav Honcharuk, Richard Veale Takahiko Kawashima, Tadashi Isa, Jun Miyata

6th research area meeting of the unified theory (Sapporo, Japan), 2025

JSNS (Niigata, Japan), 2025

Poster
2024

Evaluating a Deep Saliency Model on real-world egocentric data

Vladyslav Honcharuk, Tadashi Isa, Richard Veale

JSNS (Fukuoka, Japan), 2024

Poster
2024

Guided tour of DeepSpaceDB, a spatial transcriptomics database

Vladyslav Honcharuk, Alexis Vandenbon

NGS EXPO (Osaka, Japan), 2024

LiMe retreat (Otsu, Japan), 2024

Poster

Research Interests

Highlights of ongoing work and key areas of focus.

Spatial Transcriptomics

Development of DeepSpaceDB, a spatial transcriptomics database for interactive analysis of tissues and tissue microenvironments. Analysis of single-cell and spot resolution data.

Python Bioinformatics Data Analysis Web Development

Eye-Tracking Data Analysis

Detection of schizophrenia through eye-tracking using dynamic stimulus, analysis of egocentric eye-tracking data to understand human attention patterns and cognitive processes.

Machine Learning Computer Vision Signal Processing Python

Reinforcement Learning

Modeling of risk preferences in gambling tasks using Machine Learning. Understanding decision-making processes and behavioral patterns through computational models.

Reinforcement Learning Python Statistical Modeling Behavioral Analysis

Bioinformatics

RNA sequence and 3D structure analysis for drug development. Computational analysis of biological data to support therapeutic development and molecular understanding.

Bioinformatics RNA Analysis Drug Development Structural Biology

Skills

Programming Languages

Python (Pandas, NumPy, SciPy, Sklearn, Matplotlib, Plotly, TensorFlow, PyTorch, Flask) JavaScript R Bash C++ C

Technologies

OpenCV Docker Git GitHub SQL NoSQL GNU/Linux HTML CSS

Languages

English (Fluent) Ukrainian (Fluent) Russian (Fluent) Japanese (Beginner)

Memberships

Japan Neuroscience Society

Professional Certifications & Achievements

Certificates

Professional Certificate in Data Engineering

Massachusetts Institute of Technology

Issued: Feb 2023

Credential ID: 68420632

Statistics with Python Specialization

Coursera

Issued: Jun 2022

Credential ID: FA9QM46AAN2G

Hackathons

HACK SPF 2023 ML Winner (2nd Place)

Taras Shevchenko National University of Kyiv

Issued: Apr 2023

Machine Learning Competition

CSC Hackathon 2023 Finalist

Hackathon Expert

Issued: Jul 2023

Machine Learning Competition