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aliekhlasi/README.md

Hi, I'm Ali Ekhlasi

Postdoctoral Researcher · Department of Cognitive Sciences · University of California, Irvine

I'm a computational cognitive neuroscientist. I use fMRI, EEG and machine learning to study how the brain tells perception from imagination, how sleep supports memory, and how brain networks communicate.

🌐 aliekhlasi.com · 🆔 ORCID · 🎓 Google Scholar · ✉️ aekhlasi@uci.edu · ekhlasi.bme@gmail.com


🔬 Current work

Reflexion Lab (PI: Dr. Megan Peters), UC Irvine · 2025–present
I study perception, imagination and reality monitoring with fMRI, using neural decoding, domain adaptation, deep learning and reinforcement learning. I build reproducible, open-source pipelines to test competing theories of consciousness in the Templeton World Charity Foundation–funded ETHOS adversarial collaboration.

Previously: Sleep and Cognition (SaC) Lab (PI: Dr. Sara Mednick), UC Irvine · 2023–2024
I studied sleep and memory with EEG/polysomnography and fMRI: neural dynamics across NREM and REM sleep, and how sex hormones across the menstrual cycle regulate sleep spindles, REM activity, and emotional and working memory.

Research interests: cognitive & computational neuroscience · perception, imagery & reality monitoring · sleep & dreaming · brain networks & connectivity · neuropsychiatric disorders · machine learning & AI


🔧 Open-source tools

Project Description
SleepRhythms MATLAB toolbox that detects slow oscillations, sleep spindles and REM theta/alpha bursts in sleep EEG, with per-stage summary tables and a demo with known events
EEGChain Open-access EEGLAB-based toolbox for building, managing, automating and reproducing batch EEG processing pipelines (ICBME 2024)

📄 Selected publications

  • Ekhlasi A, Nasrabadi AM, Ahmadi H (2026). Enhanced deception detection through integrated EEG, respiration, and reaction signal analysis using optimized computational methods. Biomedical Physics & Engineering Express, 12(3). doi
  • Shuster A, Morehouse A, McDevitt E, Chen P, Whitehurst L, Zhang J, Sattari N, Uzoigwe T, Ekhlasi A, Cai D, Simon K, Niethard N, Mednick S (2025). REM refines and rescues memory representations: a new theory. SLEEP Advances, 6(1). doi
  • Ekhlasi A, Nasrabadi AM, Mohammadi MR (2023). Improving transfer entropy and partial transfer entropy for relative detection of effective connectivity strength between time series. Communications in Nonlinear Science and Numerical Simulation, 126, 107449. doi
  • Ekhlasi A, Nasrabadi AM, Mohammadi MR (2022). Analysis of EEG brain connectivity of children with ADHD using graph theory and directional information transfer. Biomedical Engineering / Biomedizinische Technik. doi
  • Ekhlasi A, Nasrabadi AM, Mohammadi MR (2021). Direction of information flow between brain regions in ADHD and healthy children based on EEG by using directed phase transfer entropy. Cognitive Neurodynamics, 15(6), 975–986. doi

➡️ Also on Google Scholar and ORCID

📚 All journal articles (12)
  1. Ekhlasi A, Nasrabadi AM, Ahmadi H (2026). Enhanced deception detection through integrated EEG, respiration, and reaction signal analysis using optimized computational methods. Biomedical Physics & Engineering Express, 12(3). doi
  2. Ekhlasi A, Hosseinzadeh MS, Ahmadi H (2025). Investigating optimal EEG channels and features for brain-computer interfaces: an exploration using evolutionary algorithms and machine learning. Frontiers in Biomedical Technologies, 12(2). doi
  3. Ekhlasi A, Nasrabadi AM, Mohammadi MR (2025). Optimal multivariate transfer entropy to determine differences in short and long-range EEG connectivity in children with ADHD and healthy children. Frontiers in Biomedical Technologies, 12(2). doi
  4. Shuster A, Morehouse A, McDevitt E, Chen P, Whitehurst L, Zhang J, Sattari N, Uzoigwe T, Ekhlasi A, Cai D, Simon K, Niethard N, Mednick S (2025). REM refines and rescues memory representations: a new theory. SLEEP Advances, 6(1). doi
  5. Ekhlasi A, Nasrabadi AM, Mohammadi MR (2023). Improving transfer entropy and partial transfer entropy for relative detection of effective connectivity strength between time series. Communications in Nonlinear Science and Numerical Simulation, 126, 107449. doi
  6. Ekhlasi A, Nasrabadi AM, Ahmadi H (2023). Detection of guilty knowledge with the combination of EEG, respiration and reaction signals. SSRN preprint. doi
  7. Ekhlasi A, Nasrabadi AM, Mohammadi MR (2022). Analysis of EEG brain connectivity of children with ADHD using graph theory and directional information transfer. Biomedical Engineering / Biomedizinische Technik. doi
  8. Ekhlasi A, Nasrabadi AM, Mohammadi MR (2021). Direction of information flow between brain regions in ADHD and healthy children based on EEG by using directed phase transfer entropy. Cognitive Neurodynamics, 15(6), 975–986. doi
  9. Ekhlasi A, Nasrabadi AM, Mohammadi MR (2021). Analysis of effective connectivity strength in children with attention deficit hyperactivity disorder using phase transfer entropy. Iranian Journal of Psychiatry, 16(4), 374. doi
  10. Ketabi H, Ekhlasi A, Ahmadi H (2021). A computer-aided approach for automatic detection of breast masses in digital mammogram via spectral clustering and support vector machine. Physical and Engineering Sciences in Medicine, 44(1), 277–290. doi
  11. Ekhlasi A, Ahmadi H, Molavi A, Nia MS, Nasrabadi AM (2021). EEG signals analysis during Ishihara's test in subjects with normal and color vision deficiency. Biomedical Physics & Engineering Express, 7(2). doi
  12. Ekhlasi A, Nasrabadi AM, Mohammadi MR (2021). Classification of the children with ADHD and healthy children based on the directed phase transfer entropy of EEG signals. Frontiers in Biomedical Technologies, 8(2), 115–122. doi
📝 Under review (4)
  1. Ekhlasi A, Olsson E, Klimova M, Huang X, Shen A, Dijkstra N, Morales J, Peters MAK. Is this the real life? Is this just fantasy? A domain adaptation framework for identifying higher-order reality representations.
  2. Adekoya T, Morehouse AB, Shuster A, Ekhlasi A, Peña AA, Zhang J, Gombert M, Alzueta E, Uzoigwe PT, Chen Y, Sattari N, Malerba P, Baker FC, Simon KC, Mednick SC. Sleep-dependent working memory across the menstrual cycle.
  3. Ekhlasi A, Morehouse A, Shuster A, Peña A, Zhang J, Gombert M, Alzueta E, Uzoigwe T, Sattari N, Malerba P, Baker F, Simon K, Mednick S. Sex hormones dynamically regulate sleep spindle expression and emotional memory bias across the menstrual cycle.
  4. Ekhlasi A, Nasrabadi AM, Ahmadi H. Multivariate phase transfer entropy (MPTE) for estimating directed connectivity in simulated and neural time series.
🗂️ Conference proceedings (12)
  1. Mohammadi Y, Rostami A, Abolghasemi S, Hoseinzadeh MS, Ekhlasi A (2024). Designing and integration of hardware and software for a remote ultrasound monitoring system. ICSPIS 2024. doi
  2. Afdideh F, Boozari M, Ekhlasi A, Nasrabadi AM (2024). EEGChain: an open-access EEGLAB-based toolbox for building, managing, automating, and reproducing batch EEG processing pipelines. ICBME 2024. doi
  3. Ekhlasi A, Ahmadi H (2022). Investigating the differences between atrial fibrillation and normal ECG signals using the EMD method. ICSPIS 2022. doi
  4. Hossein Zadeh MS, Ekhlasi A (2022). A wireless body temperature and oxygen saturation monitoring system based on Android smartphones. SCIoT 2022. doi
  5. Ekhlasi A, Hoseinzadeh MS, Ahmadi H, Ekhlasi A (2022). Development of an Ethernet-based patient remote monitoring device. DCHPC 2022. doi
  6. Bagheri P, Ahmadi H, Ekhlasi A (2020). Investigation of brain functional integration and segregation in individuals based on the quality of performing mathematical calculations. ICSPIS 2020. doi
  7. Hoseinzadeh MS, Ekhlasi A, Ahmadi H (2020). Design and implementation of a blood pressure device with high sampling frequency to analyze cardiovascular diseases in LabVIEW. ICSPIS 2020. doi
  8. Ghassemi F, Hoseinzadeh MS, Ekhlasi A (2020). Design and implementation of wireless body temperature monitor with warning system via SMS. ICSPIS 2020. doi
  9. Ekhlasi A, Moieni N, Ahmadi H, Ekhlasi A (2020). Analysis of ECG signals to classify abnormal patterns by employing artificial neural network and discrete wavelet coefficients. ICSPIS 2020. doi
  10. Ekhlasi A, Hossein Zadeh MS, Latifi M, Ahmadi H, Dehghan Y (2020). Design and implementation of a voice-controlled robot with obstacle detection for disabled people. 7th National Congress of New Findings of Iranian Electrical Engineering. doi
  11. Ahmadi H, Hossein Zadeh MS, Dehghan Y, Ekhlasi A, Latifi M (2020). Voice commands classification in order to control robot movement. 3rd International Conference on Technology Development in Electrical Engineering of Iran. doi
  12. Ahmadi H, Ekhlasi A (2019). Types of EMD algorithms. ICSPIS 2019. doi
🖼️ Conference posters (10)
  1. Ekhlasi A, Olsson E, Klimova M, Huang X, Shen A, Dijkstra N, Morales J, Peters MAK. Is this the real life? Is this just fantasy? A domain adaptation framework for identifying higher-order reality representations. Cognitive Computational Neuroscience (CCN 2026), New York, May 2026.
  2. Ekhlasi A, Olsson E, Klimova M, Huang X, Shen A, Dijkstra N, Morales J, Peters MAK. How does your brain know what's real? Domain adaptation and fMRI approaches to revealing the neural mechanisms of reality monitoring. Vision Sciences Society (VSS), St. Pete Beach, FL, May 2026.
  3. Huang X, Shen A, Olsson E, Ekhlasi A, Klimova M, Yurdakul OC, Peters MAK, Morales J. What we talk about when we talk about vividness. VSS, St. Pete Beach, FL, May 2026.
  4. Yurdakul OC, Huang X, Shen A, Olsson E, Ekhlasi A, Klimova M, Morales J, Peters MAK. Quantifying vividness reports using Gaussian process regression. VSS, St. Pete Beach, FL, May 2026.
  5. Ekhlasi A, Olsson E, Klimova M, Huang X, Shen A, Garcia K, Dijkstra N, Morales J, Peters MAK. Reproducible and open-source fMRI decoding pipelines for arbitrating theories of consciousness. Society for Neuroscience (SfN), San Diego, CA, November 2025.
  6. Ekhlasi A, Shuster A, Morehouse A, Uzoigwe P, Sattari N, Zhang J, Gombert M, Baker F, Simon K, Malerba P, Mednick S. Sex hormones shape spindle activity across the menstrual cycle. SLEEP 2025 (APSS), Seattle, WA, June 2025.
  7. Chen Y, Shuster A, Morehouse A, Uzoigwe P, Adekoya T, Ekhlasi A, Zhang J, Sattari N, Gombert M, Baker F, Simon K, Mednick S. REM EEG events are modulated by menstrual cycle and sex hormones. SLEEP 2025 (APSS), Seattle, WA, June 2025.
  8. Morehouse A, Shuster A, Pena A, Zhang J, Ekhlasi A, Sattari N, Gombert M, Alzueta E, Baker F, Simon K, Mednick S. How does the menstrual cycle affect overnight emotional memory consolidation? SLEEP 2025 (APSS), Seattle, WA, June 2025.
  9. Adekoya T, Shuster A, Morehouse A, Uzoigwe P, Chen Y, Ekhlasi A, Zhang J, Sattari N, Gombert M, Baker F, Simon K, Mednick S. Sleep-dependent working memory across the menstrual cycle. SLEEP 2025 (APSS), Seattle, WA, June 2025.
  10. Afdideh F, Boozari M, Ekhlasi A, Nasrabadi AM. EEGChain: an open-access EEGLAB-based toolbox for building, managing, automating, and reproducing batch EEG processing pipelines. ICBME 2024.
🎤 Talks (3)
  1. Oral presentation, Metacognitive Science Satellite Meeting, Cognitive Computational Neuroscience (CCN) 2026, Columbia University, New York, August 2026.
  2. Oral presentation, 10th Annual UC Irvine Postdoctoral Scholar Research Symposium, April 2026. 🏆 Oral Presentation Award.
  3. Invited colloquium speaker, Department of Cognitive Sciences, University of California, Irvine, March 2026.

🎤 Recent talks & highlights

  • 🏆 Oral Presentation Award, 10th Annual UC Irvine Postdoctoral Scholar Research Symposium (2026)
  • Oral presentation, Metacognitive Science Satellite Meeting, CCN 2026, Columbia University (2026)
  • Invited colloquium, Department of Cognitive Sciences, UC Irvine (2026)
  • Posters at CCN 2026, VSS 2026, SfN 2025 and SLEEP 2025

🧑‍🏫 Teaching, mentoring & service

  • Lecturer & thesis advisor, Department of Biomedical Engineering, Azad University, Science and Research Branch, Tehran (2016–2023). Courses include Introduction to Statistical Learning, Neural Analytics, Machine Learning and Data Mining, Bioelectric Phenomena and Principles of Medical Imaging Systems
  • Guest lecturer, "Neural Data Analysis" (COGS 108), UC Irvine (2025)
  • Mentoring: Since the second year of my Ph.D., I have supervised six undergraduate researchers and co-supervised four graduate and doctoral students. All six undergraduates contributed to projects that led to conference publications and went on to graduate studies; the graduate students also contributed to conference publications and a peer-reviewed journal article. During my first postdoctoral appointment at UC Irvine, I took on additional responsibility for mentoring graduate researchers and supporting their projects, particularly while my supervisor was on sabbatical. In my current position, as a senior researcher in the lab, I lead the training of five research assistants in fMRI data collection and preliminary analysis.
  • Reviewer for Scientific Reports, Neural Computing and Applications, Brain Structure and Function, Applied Psychophysiology and Biofeedback, and Signal, Image and Video Processing
🎓 Workshops, seminars & guest lectures

Guest lectures (U = undergraduate, G = graduate)

  • "Neural Data Analysis", COGS 108, Department of Cognitive Sciences, University of California, Irvine (2025) [U]
  • "Principles of Cognitive Neuroscience", Azad University, Science and Research Branch (2021) [G]

Workshops & seminars (lecturer and organizer)

  • "The Addicted Brain", Azad University, Science and Research Branch (2021)
  • "Gamification", two-day seminar, Azad University, Science and Research Branch (2020)
  • "Practical Workshop on Introduction to the Health and Medical Centers", 14 sessions, Azad University, Science and Research Branch (2020)
  • "Brain Physiology and Cognition", 8 sessions, Azad University, Central Tehran Branch (2019)
📜 Training & certifications

Teaching, mentoring & academic career development

  • Mentoring Excellence Program, UC Irvine Graduate Division (Fall 2025)
  • Improv for Teaching, UC Irvine Graduate Division (Summer 2025)
  • Public Speaking: Activate to Captivate Certificate Program, UC Irvine Graduate Division (Summer 2025)
  • Launching Your Academic Job Search, UC Irvine Graduate Division (Summer 2024)
  • Preparing for a Faculty Career, UC Irvine Graduate Division (Summer 2026)

Research development, grant writing & ethics

  • ICTS K-Club Grant Writing Series, Institute for Clinical and Translational Science (ICTS), UC Irvine (Fall 2025)
  • CITI Program: Responsible Conduct of Research (RCR) and Human Subjects Research training: Biomedical Investigators; Human Subjects Research Considerations and Big Data Research; Social/Behavioral Investigators

Machine learning & computational methods

  • Deep Learning Specialization, DeepLearning.AI (Summer 2025)
  • Online BCI & Neurotechnology Spring School, g.tec medical engineering GmbH (2021)
  • Brain Signal Processing and its Application in Computational Neuroscience, National Brain Mapping Lab of Iran (2017)

Neuroscience & biomedical engineering

  • The Brain and Space, Duke University, Duke Institute for Brain Sciences (Prof. Jennifer M. Groh), Coursera (2016)
  • The Addicted Brain, Emory University (Prof. Michael Kuhar), Coursera (2017)
  • Bioelectricity: A Quantitative Approach, Duke University, Duke Institute for Brain Sciences (Prof. Roger Barr), Coursera
  • Introduction to Biomedical Imaging, University of Queensland, UQx BIOIMG101x, edX
  • Introduction to Cognitive Neuroscience, Iranian Neuroscience Society (2015)

Technical & professional training

  • Technical Supervisor of Medical Equipment Manufacturer, Department of Medical Equipment, Ministry of Health and Medical Education of Iran (2013)
  • Gamification, University of Pennsylvania, The Wharton School (Prof. Kevin Werbach), Coursera (2016)

🛠️ Skills

Languages & tools: MATLAB · Python · R · SPSS · LabVIEW · Git · Linux/HPC · GPU computing
Machine learning: PyTorch · TensorFlow · classical ML · deep learning (CNN/RNN/GNN) · generative AI / LLMs · domain adaptation · neural decoding
Neuroimaging & signals: fMRI (fMRIPrep, SPM, Nilearn, Neurodesk) · EEG/PSG (EEGLAB, Functional Connectivity Toolbox) · ECG, EMG, GSR, PPG, respiration


🎓 Education

  • Ph.D., Biomedical Engineering (Computational Neuroscience), Azad University, Science and Research Branch, Tehran (2021). Advisors: Dr. Ali Motie Nasrabadi, Dr. Mohammadreza Mohammadi
  • M.Sc., Biomedical Engineering (Computational Neuroscience), Shahed University, Tehran (2014). Advisor: Dr. Ali Motie Nasrabadi
  • B.Sc., Biomedical Engineering (Bioelectric), Azad University, Science and Research Branch, Tehran (2011)

Popular repositories Loading

  1. aliekhlasi aliekhlasi Public

  2. EEGChain EEGChain Public

    EEGChain: An Open-Access EEGLAB-based Toolbox for Building, Managing, Automating, and Reproducing Batch EEG Processing Pipelines

    MATLAB

  3. SleepRhythms SleepRhythms Public

    SleepRhythms: MATLAB toolbox for detecting slow oscillations, sleep spindles and REM theta/alpha bursts in sleep EEG (Sleep and Cognition (SaC) Lab)

    MATLAB

  4. ethos-da-reality-content-searchlight ethos-da-reality-content-searchlight Public

    Domain-adaptation searchlight (Subspace Alignment) for reality and content signals in perception vs. imagery fMRI. Part of the ETHOS adversarial collaboration.

    Python