Marjan Stoimchev / CV·ML Engineer
Open to roles Résumé
Open to CV/ML Engineer · Applied Scientist · R&D

Marjan Stoimchev

Computer Vision & Machine Learning Engineer

building production vision systems

I'm an R&D engineer who turns research ideas into scalable, production-ready AI across computer vision, multimodal and vision-language models, and large-scale learning. I focus on two hard problems: getting strong results when labeled data is scarce, and making inference pipelines fast and robust enough to deploy.

Ljubljana, Slovenia · Open to full-time roles · Remote or Relocation
7+
Years in AI R&D
Research-to-production across computer vision, multimodal & ML systems
PhD
Computer Vision & Deep Learning
R&D engineer bridging academic research and industry delivery
WeeksMin
Faster, automated pipelines
Self-supervised embedding workflows for clinical phenotyping at MedAI
Label-efficient
Less manual annotation
Self-/semi-supervised learning and foundation-model adaptation
Experience

Where I've shipped

From a national geospatial AI initiative to clinical decision-support: research-grade ideas turned into systems that run.

  1. Computer Vision / ML Engineering Consultant · Independent Consultancy
    Apr 2026 – Present
    Production segmentation and annotation systems for inventory image analysis.
    • Built an end-to-end segmentation-assisted annotation pipeline covering model training, inference integration, evaluation scripts, reproducible configs, and technical documentation.
    • Distilled a DINOv3-style teacher into a lightweight YOLOv9 student, transferring task-specific representations for fast proposal generation and annotation assistance.
    • Stood up a self-hosted CVAT environment and designed the full import → review → correct → export workflow around it.
    • Implemented active-learning triage that prioritizes images by confidence, entropy, and disagreement scoring so annotators spend time where it matters.
    • Engineered boundary-aware pseudo-mask refinement to cut mask leakage, holes, jagged edges, and under-segmentation, plus a synthetic image-mask generation pipeline and cross-frame temporal consistency.
    • Refactored, documented, and containerized the codebase for reproducibility and clean handoff.
    YOLOv9DINOv3CVATActive LearningSynthetic DataDocker
  2. Computer Vision Engineer · MedAI
    Nov 2024 – Present
    Replacing manual clinical phenotyping workflows with high-speed self-supervised AI.
    • Compressed prediction wait times from weeks to minutes by building self-supervised embedding pipelines for clinical phenotyping.
    • Solved the labeled-data bottleneck with DINOv2/v3 and MAE self-supervised models for multiplex immunofluorescence.
    • Shipped production pipelines for spatial clustering and neighborhood analysis, integrated into clinical decision-support prototypes.
    • Improved cell-type identification accuracy and cut manual annotation time by roughly 20%, translating model outputs into explainable biological insights for stakeholders.
    DINOv2/v3MAESelf-SupervisedDigital PathologyClinical Decision Support
  3. PhD Research Scientist · Jožef Stefan Institute, Dept. of Knowledge Technologies
    Oct 2021 – Dec 2025
    Novel architectures built from scratch, plus the reproducible engineering standards to run them.
    • Designed and built novel graph-based ViT+GNN architectures from scratch to model label dependencies for hierarchical, structured prediction.
    • Developed SSL-MAE, a semi-supervised masked-autoencoder framework that learns strong representations from largely unlabeled remote-sensing imagery.
    • Established the lab's standard for reproducible research: modular, multi-GPU pipelines in PyTorch Lightning and Hydra, later adopted by intern teams.
    • Led MSc interns in refactoring experimental research code into clean, executable pipelines across remote sensing and materials science.
    PyTorch LightningHydraMulti-GPUViT + GNNSemi-Supervised
Selected work

Projects & case studies

Problem → approach → outcome. A cross-section of systems spanning satellites, slides, and microscopes.

Geospatial AI

Slovenia Data Cube & AI Factory

Problem

The national Slovenian AI Factory needed analysis-ready geospatial data instead of raw, hard-to-consume archives.

Approach

Leading development of the national Slovenia Data Cube, analysis-ready, high-performance geospatial data infrastructure.

Impact

A shared, performant foundation for geospatial AI across the Slovenian AI Factory initiative.

Earth ObservationData CubeGeospatial Infra
Remote Sensing

GeoAI Foundation Models

Problem

Remote-sensing tasks tend to start from scratch, with little representation reuse across segmentation and detection.

Approach

Training foundation models for remote sensing via multi-task and self-supervised paradigms, producing reusable backbones.

Impact

Backbones power both semantic segmentation and object detection, sharing representation learning across tasks.

Foundation ModelsSelf-SupervisedMulti-Task
Earth Observation

Multi-Source Data Fusion

Problem

Optical satellite imagery alone leaves gaps; clouds and lighting limit what a single sensor sees over time.

Approach

Temporal and multi-modal fusion of Sentinel-1 radar and Sentinel-2 optical imagery.

Impact

Complementary radar and optical signals combine for more robust analysis across time.

Sentinel-1Sentinel-2Multi-Modal
Representation Learning

Masked Prototype Prediction

Problem

Strong vision representations usually demand large labeled datasets many domains simply don't have.

Approach

Self-supervised representation learning combining DINO-style student-teacher training with MAE-style encoders.

Impact

Learns transferable representations without labels, the backbone strategy behind much of my label-efficient work.

Self-SupervisedDINOMAE
Digital Pathology

Zero-Shot Nuclei Segmentation

Problem

Expert annotation of nuclei in pathology slides is slow, costly, and a bottleneck for downstream analysis.

Approach

Zero-shot SAM-based nuclei detection that requires no task-specific labels.

Impact

Reduces the expert annotation burden for digital-pathology workflows.

SAMZero-ShotSegmentation
Medical Imaging

Whole-Slide Embedding Analysis

Problem

Whole-slide images are massive; extracting clinically meaningful structure at scale is hard.

Approach

DINOv2/v3/MAE embedding pipelines on multi-GPU with mixed precision, feeding cell-type clustering and survival analysis.

Impact

Turns gigapixel slides into cell-type clusters and survival signals through scalable, efficient pipelines.

DINOv2/v3Multi-GPUSurvival Analysis
Microscopy

STEM Microscopy Drift Correction

Problem

Sample drift during STEM microscopy degrades image quality and traditionally needs manual correction.

Approach

A vision-based autoencoder that performs automated drift correction in STEM microscopy.

Impact

Automates a correction step that would otherwise be manual and error-prone.

AutoencoderMicroscopyImage Restoration
From experiment to production

How I ship

The engineering discipline behind the models, reproducible from first commit to deployed artifact.

01 · Build

Train

PyTorchLightningHydra
02 · Observe

Track

MLflowWeights & Biases
03 · Scale

Distribute

Multi-GPUMixed PrecisionHPC / Slurm
04 · Package

Containerize

DockerReproducible configs
05 · Deploy

Export

ONNXTensorRT
Tech toolbox

Skills & stack

The capabilities and exact tooling I reach for, from exploratory research to reliable deployment.

Geospatial AI & Foundation Models

Pretraining and adapting vision foundation models, with a bias toward learning from limited labels.

ViTMAEDINO / DINOv3Self-SupervisedSemi-SupervisedLabel-Efficient Learning

Multimodal & Vision-Language

Bringing vision together with language and other modalities into unified models.

Vision-Language Models (VLMs)Multimodal LearningImage-Text AlignmentCross-Modal RetrievalGenerative AI

Segmentation & Annotation Systems

End-to-end annotation tooling, from pseudo-labeling and refinement to active-learning triage.

YOLOv9SAM Pseudo-LabelingPseudo-Mask RefinementSynthetic Image-MaskActive LearningCVAT

Structured & Multi-Task Learning

Modeling label structure and dependencies for hierarchical, multi-label, and multi-task prediction.

Hierarchical / Multi-LabelLabel Dependency ModelingGNNsWeak / Noisy SupervisionMulti-Task

Software Engineering & ML Systems

Scalable, reproducible training and inference pipelines built to deploy and hand off.

PythonPyTorchLightningMulti-GPUMLflowW&BHPC / SlurmDockerONNX / TensorRT

Foundations & Tooling

The day-to-day libraries and tooling behind data, modeling, and experimentation.

NumPySciPyPandasscikit-learnOpenCVTorchGeoPyGTransformersGitLaTeX

Domains

Where I've shipped vision systems and learned what production really demands.

Earth ObservationRemote SensingInventory ImagingMedical ImagingMicroscopyDigital Pathology
Depth behind the engineering

Research & publications

Peer-reviewed work across IEEE and MDPI venues. The rigor that underpins the systems I build.

Selected journal articles
Code on GitHub Full list on Scholar
IEEE JSTARS2025

SSL-MAE: Adaptive Semisupervised Learning Framework for Multilabel Classification of Remote Sensing Images Using Masked Autoencoders

M. Stoimchev, J. Levatić, D. Kocev, S. Džeroski · vol. 18, pp. 14882–14896

IEEE TGRS2024

Semi-Supervised Multi-Label Classification of Land Use/Land Cover in Remote Sensing Images With Predictive Clustering Trees and Ensembles

M. Stoimchev, J. Levatić, D. Kocev, S. Džeroski · vol. 62, pp. 1–16, Art. 4706416

Remote Sensing2023

Deep Network Architectures as Feature Extractors for Multi-Label Classification of Remote Sensing Images

M. Stoimchev, D. Kocev, S. Džeroski · vol. 15(2):538

MDPI Sensors2022
Prešern Award

Learning to Combine Local and Global Image Information for Contactless Palmprint Recognition

M. Stoimchev, M. Ivanovska, V. Štruc · vol. 22(1):73

About

From PhD research to shipping systems

I hold a PhD in Computer Vision and Deep Learning and work as an R&D engineer focused on turning research ideas into scalable, production-ready systems. My work addresses two recurring challenges in real-world AI: data scarcity and slow, fragile inference pipelines.

I translate deep AI research into reproducible, deployment-ready ML pipelines.

I design learning frameworks that reduce dependence on labeled data, build automated analysis workflows that minimize manual expert effort, and engineer efficient training and deployment pipelines for large-scale biological and remote-sensing datasets. Increasingly my work spans modalities, combining images with text through multimodal learning and vision-language models (VLMs), and I'm comfortable taking ideas from early research through to robust deployment in high-performance computing environments.

I enjoy working at the intersection of computer vision, multimodal and vision-language AI, medical imaging, remote sensing, and materials science, where robustness and interpretability matter as much as raw accuracy.

Let's talk

Let's build something that ships

I'm open to Computer Vision / ML Engineer, Applied Scientist, and R&D roles, remote or relocation. If you need vision systems that move from prototype to production, let's talk.