About me

Here’s a brief overview of my career, along with my current and past research focus:

2023 - Current: Research Professor, Ghent University Global Campus, South Korea

Research focus

• (B.img) Biomedical imaging
• (B.inf) Bioinformatics
• (XAI) Trustworthy and explainable AI
• (SSL) Image-based self-supervised learning

Senior author publications

• (B.img) Color Flow Imaging Microscopy Improves Identification of Stress Sources of Protein Aggregates in Biopharmaceuticals
  2024, MICCAI - MOVI Workshop
• (B.img) Exploring Patient Data Requirements in Training Effective AI Models for MRI-based Breast Cancer Classification
  2024, MICCAI - Deep Breath Workshop
• (B.img-XAI-SSL) Evaluating Visual Explanations of Attention Maps for Transformer-Based Medical Imaging
  2024, MICCAI - iMIMIC Workshop
• (B.img-XAI-SSL) Identifying Critical Tokens for Accurate Predictions in Transformer-based Medical Imaging Models
  2024, MICCAI - MLMI Workshop

First author publications

• (SSL) Self-Supervised Benchmark Lottery on ImageNet: Do Marginal Improvements Translate to Improvements on Similar Datasets?
  2024, IEEE IJCNN, oral presentation
• (B.inf) Assessing the Reliability of Point Mutation as Data Augmentation for Deep Learning with Genomic Data
  2024, BMC Bioinformatics

2022 - 2023: Postdoctoral Fellow, Ghent University Global Campus, South Korea

First author publications

• (SSL) Know Your Self-supervised Learning: A Survey on Image-based Generative and Discriminative Training
  2023, Transactions on Machine Learning Research
• (B.inf) BRCA Gene Mutations in dbSNP: A Visual Exploration of Genetic Variants
  2023, Arxiv
• (B.inf-XAI) Mutate and Observe: Utilizing Deep Neural Networks to Investigate the Impact of Mutations on Translation Initiation
  2023, Bioinformatics, Oxford Press
• (B.inf-XAI) Utilizing Mutations to Evaluate Interpretability of Neural Networks on Genomic Data
  2023, NeurIPS - LMRL Workshop

Repositories:

• (B.inf) github.com/utkuozbulak/mutate-and-observe

2017 - 2022: PhD in Computer Science, Ghent University, Belgium

Research focus

• (Adversarial) Adversarial examples: attacks, defenses, and properties

First author publications

• (Adversarial) Prevalence of Adversarial Examples in Neural Networks: Attacks, Defenses, and Opportunities
  2022, Ghent University, PhD thesis
• (Adversarial-XAI) Evaluating Adversarial Attacks on ImageNet: A Reality Check on Misclassification Classes
  2022, NeurIPS - Workshop on ImageNet: Past, Present, and Future
• (Adversarial) Selection of Source Images Heavily Influences the Effectiveness of Adversarial Attacks
  2021, BMVC, oral presentation
• (Adversarial-XAI) Investigating the Significance of Adversarial Attacks and Their Relation to Interpretability for Radar-based Human Activity Recognition Systems
  2021, Computer Vision and Image Understanding, Elsevier
• (Adversarial) Regional Image Perturbation Reduces Lp Norms of Adversarial Examples While Maintaining Model-to-model Transferability
  2020, ICML - UDL Workshop
• (Adversarial) Perturbation Analysis of Gradient-based Adversarial Attacks
  2020, Pattern Recognition Letters, Elsevier
• (Adversarial-B.img) Impact of Adversarial Examples on Deep Learning Models for Biomedical Image Segmentation
  2019, MICCAI, poster presentation
• (Adversarial) Not All Adversarial Examples Require a Complex Defense: Identifying Over-optimized Adversarial Examples with IQR-based Logit Thresholding
  2019, IEEE IJCNN, oral presentation
• (Adversarial) How the Softmax Output is Misleading for Evaluating the Strength of Adversarial Examples
  2018, NeurIPS - SecML Workshop

Repositories

• (XAI) github.com/utkuozbulak/pytorch-cnn-visualizations
• (Adversarial) github.com/utkuozbulak/adaptive-segmentation-mask-attack
• (Adversarial) github.com/utkuozbulak/pytorch-cnn-adversarial-attacks
• (Adversarial) github.com/utkuozbulak/imagenet-adversarial-image-evaluation
• (Adversarial) github.com/utkuozbulak/regional-adversarial-perturbation
• (Other) github.com/utkuozbulak/pytorch-custom-datasets

2016 - 2017: MSc. in Data Science, University of Southampton, UK

2014 - 2016: SAP Business Intelligence Consultant, Acron Consulting, Turkey

Notable clients

• The Coca Cola Company
• Turkish Airlines
• Bosch Siemens Hausgerate
• Flormar Cosmetics

2012 - 2014: BSc. in Computer Engineering, Yasar University, Turkey