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JonathanGuerne/README.md

Hi there, I'm Jonathan Guerne 👋

I'm a PhD student in Computer Science at the University of Neuchâtel and HE-Arc, supervised by Prof. Dr. Paul Cotofrei (University of Neuchâtel) and Prof. Dr. Hatem Ghorbel (HE-Arc).

My research sits at the intersection of large language models (LLMs) and neurodegenerative disease research. Through my thesis, CogniLens, I investigate whether language models can be used to simulate the functional cognitive effects of Alzheimer's disease (AD) and to support its early detection and monitoring.


🔬 The CogniLens thesis

CogniLens is a framework for systematically altering language models to simulate Alzheimer's-related cognitive decline, evaluated through both behavioral and neural alignment metrics:

  • Cognitive assessment — an adaptation of the Montreal Cognitive Assessment (MoCA) into structured text-based prompts with pairwise comparison metrics, enabling continuous quantification of cognitive performance across attention, memory, language, and abstraction.
  • Model alteration — three strategies to simulate cognitive decline: baseline neuron ablation, transcript-based fine-tuning on AD speech data, and neurobiologically informed targeted layer alterations grounded in brain region-to-model-layer mappings.
  • Neural alignmentbrain score, a measure of alignment between model internal representations and human fMRI recordings, computed at each stage of alteration to evaluate the neural plausibility of the simulated decline.

🧠 Research interests

  • LLM evaluation & cognitive assessment
  • Alzheimer's disease detection from linguistic data
  • Model interpretability & neural alignment (brain score)
  • Digital twins of cognitive decline
  • Brain–language mapping (fMRI ↔ model representations)

📚 Selected publications

  • COGNILENS: Analyzing Cognitive Decline in Language Models for Alzheimer's Monitoring — EACL 2026 Student Research Workshop (ACL Anthology)
  • RAG: Unveiling the Power of Retrieval-Augmented Generation — SwissText 2024 (ACL Anthology)
  • Creating a virtual receptionist to lighten your employees' workload: a case study with the canton of Jura and subsidies for training — SwissText 2024 (ACL Anthology)

🔗 Links

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  1. thatcoinflip thatcoinflip Public

    The coin flip software is a user-friendly tool designed to simulate the random toss of a coin. Its ability to generate random outcomes ensures an unbiased approach, allowing for fair and transparen…

    HTML 2

  2. MoodBot MoodBot Public

    A discord bot able to give users emotion (mood) based on their send messages

    Python 1

  3. GameOfLife GameOfLife Public

    Simple Game of life Implementation with PyGame

    Python

  4. MiniGames MiniGames Public

    collections de minis jeux jouables en multiplatteforme et en réseau

    Java 1

  5. NBA_MLBD NBA_MLBD Public

    Predict NBA player position using Machine Learning based on there stats per game

    Jupyter Notebook 1

  6. HE-Arc/livre-python HE-Arc/livre-python Public archive

    Livre collaboratif autour de Python

    Python 13 33