AM Ali Mikaeili
Frankfurt, Germany

Ali
Mikaeili

AI Researcher working at the intersection of machine learning and neuroscience.

I build learning systems for connectomics at the Max Planck Institute for Brain Research, including unsupervised synapse analyses and cell classification from 3D electron microscopy. My work spans representation learning, applying AI methods on large scale biological data, and the question of how artificial and biological intelligence inform one another.

Dept. of Neural Systems · Prof. Gilles Laurent
M.Sc. AI & Robotics · University of Tehran
Email GitHub LinkedIn
Portrait of Ali Mikaeili
Focus AI × Neuroscience
01

Selected Research

5 papers · 4 published
Published
  1. 01

    Attention-Based Segmentation of Brain Tumors Using Feature-Level Fusion and a UNet Architecture

    Ali Mikaeili Barzili, Behzad Moshiri

    IEEE AREE 2025
  2. 02

    Detection of Autism Spectrum Disorder Using Quantum Support Vector Machines

    A. E. Zadeh, Ali Mikaeili Barzili, Mohammad Reza Nemati, Mohammad Khoshnevisan, Hamid Azadegan, Behzad Moshiri

    IEEE AI2E 2025
  3. 03

    MedFedPure: A Medical Federated Framework with MAE-Based Detection and Diffusion Purification for Inference-Time Attacks

    Mohammad Karami, Mohammad Reza Nemati, Aidin Kazemi, Ali Mikaeili Barzili, Hamid Azadegan, Behzad Moshiri

    arXiv 2025
  4. 04

    SpikeReg: Energy-Efficient 3D Deformable Medical Image Registration with Spiking Neural Networks

    Ali Mikaeili Barzili, Behzad Moshiri, Hamid Azadegan, Mohammad-Reza A. Dehaqani

    arXiv 2026
Under Review
  1. 05

    LiquidReg: An Adaptive ODE Engine for Deformable Registration

    Ali Mikaeili Barzili, Behzad Moshiri

    In review
02

Experience

4 positions

  1. Research Assistant

    Now

    Max Planck Institute for Brain Research · Frankfurt

    Unsupervised synapse clustering via contrastive learning on 3D electron-microscopy data, and cell classification with Vision Transformers.

    Contrastive LearningVision TransformersConnectomics
    2024 — present

  2. Data Analyst

    Hamrahe Aval (MCI), R&D · Tehran

    Text-to-speech and speech emotion recognition for the GITEX exhibition; product manager for the Persian interactive dog-robot project.

    TTSSpeech EmotionProduct Management
    2023 — 2024

  3. Teaching Assistant

    University of Tehran · Dept. of CS & EE

    Led four AI medical-imaging research teams; assisted in Statistical Inference and Artificial Intelligence courses.

    Medical ImagingResearch LeadershipDeep Learning
    2023 — 2024

  4. Teaching Assistant

    Payame Noor University · Ardabil

    Data Structures, Algorithms, Artificial Intelligence, and Operating Systems labs and assessments.

    AlgorithmsAIOperating Systems
    2020 — 2023
03

Projects

github.com/alim98
🦑

Cuttlefish Synapse Clustering

Clustering and analyzing 3D synapse structures from cuttlefish electron-microscopy data via contrastive learning (MPIBR).

Contrastive Learning3D EMPyTorch
⚡

SpikeReg

Deformable brain registration with Spiking Neural Networks — an energy-efficient alternative.

SNNMedical ImagingUNet
🌊

LiquidReg

Deformable registration via Liquid Time-constant Networks and continuous-time ODE solvers.

LTCODEDiffeomorphic
04

Notes & Writing

study notes
∫
Gaussian Processes MLSS 2015 · Neil Lawrence

Gaussian Processes: Intuition & Mathematics

A full synthesis of Neil Lawrence's GP lecture — from Laplace's Demon and the philosophy of probability, through kernel functions and conditioning, to non-Gaussian likelihoods and parameter optimization.

Kernel FunctionsBayesian InferenceMarginalizationEP vs VariationalInteractive Demos
+

More notes coming soon

Currently studying and synthesizing additional lectures.

05

Skills & Education

AI & Machine Learning
Representation LearningContrastive LearningSpiking Neural NetworksVision TransformersDiffusion ModelsGANsNLP · BERT · RAGVLMs
Neuroscience
ConnectomicsWebKnossosMedical Image AnalysisDeformable Registration
Programming
PythonC / C++JavaKotlinFlutter
Frameworks & Tools
PyTorchTensorFlowScikit-LearnNumPy · PandasDockerGitLinuxLaTeX
Languages
🇬🇧 English — Advanced🇮🇷 Persian — Native🇦🇿 Azerbaijani — Native🇹🇷 Turkish — Advanced
Education
M.Sc. Artificial Intelligence & Robotics

University of Tehran · 2023–2025 · 17/20

Thesis — SpikeReg: A Spiking-UNet for Deformable Registration

B.Eng. Computer Engineering

Payame Noor University · 2020–2023 · 16.5/20

B.Sc. Educational Sciences

Farhangian University · 2017–2021 · 17.5/20