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yacine-baghli/README.md

Hey, I'm Yacine 👋

ML Researcher — Generative Models · Computational Biology · Agentic AI

I build models that learn the structure of noise and agents that act in the real world.
Currently finishing my MSc thesis at IETR CentraleSupélec Université Paris-Saclay on discrete diffusion for DNA sequence reconstruction, and working as a Research Assistant at MBZUAI (Zhao Lab) on single-cell computational biology for autoimmune diseases.

📍 France · Open to Research & Industry — Available August 2026

Website LinkedIn Email


🔬 Research

Project What it does Status
TraceDiffMSc Thesis Discrete diffusion model that learns structured noise (insertions, deletions, substitutions) in DNA sequences. Alignment-marginalizing encoder with attention pooling. State-of-the-art on Clustered Nanopore Reads. 📝 Manuscript in prep (NeurIPS/ICML workshop)
T-Cell Atlas for MSMBZUAI Single-cell atlas integrating longitudinal scRNA-seq (EAE mouse + human MS data). Clustering, trajectory analysis, and differential expression with Scanpy. 🔄 Ongoing

🛠️ Selected Projects

World model bridging digital perception and biological computation — CNN encoder + DishBrain-inspired spiking neural network (LIF neurons, STDP plasticity).

World Models Spiking Networks STDP

8 Transformer attention mechanisms (MHA, GQA, MQA, SWA, DiffAttn, MLA, MoH, NSA) implemented from scratch. Controlled pre-training on FineWeb-Edu with 42 unit tests.

Transformers PyTorch From Scratch

Production pipeline generating synthetic DNA datasets calibrated to 7 synthesis platforms × 3 sequencing backends (Illumina, Nanopore, PacBio). 3-layer error injection.

Noise Modeling Bioinformatics MIT License

LLM-driven multi-agent clinical platform — automated API orchestration across NCBI, PubMed, ClinVar. Real-time variant annotation and pathogenicity scoring.

Multi-Agent Genomics FastAPI

Persistent multi-agent customs clearance system — 3 chained Gemini primitives: live supplier calls, persistent case memory, computer-use portal navigation. Built at RAISE Summit × Google DeepMind.

Multi-Agent Gemini Computer Use

VLM + SLAM spatial mapping + cross-session knowledge persistence on Unitree Go2. Built at HACK 2026 — ETH Zurich Robotics Club (selected from 500+ applicants).

VLMs SLAM Embodied AI

🏆 Highlights

  • 🥈 2nd Place — EPFL Quantum Hackathon (Quantum ML for option pricing, QRC for stock prediction)
  • 🧬 RAISE Summit × Google DeepMind — Multi-agent customs clearance system
  • 🏥 SOPHiA Genetics × ETH Zurich — AI for Health Hackathon
  • 🤖 HACK 2026 — ETH Zurich Robotics Club — Embodied multimodal agent on Unitree Go2

🎓 Education

MSc Engineering — Polytech Nancy, Université de Lorraine Intelligent & Autonomous Systems · Thesis at CentraleSupélec
Exchange — ÉTS Montréal Computer Vision & Signal Processing
CPGE — Université de Lorraine Mathematics & Computer Science

🧰 Tech Stack

Research       Diffusion Models · Transformers · World Models · Agentic AI · Self-Supervised Learning
               Representation Learning · Foundation Models · Spiking Networks · Clinical ML

Stack          Python · PyTorch · CUDA · C/C++ · BF16/FP16 · Multi-GPU · Scanpy · FastAPI

Methods        Ablation Studies · Controlled Experiments · Reproducible Research · Open Source

Building models that understand structure, not just data.

Pinned Loading

  1. bio-wm bio-wm Public

    A research prototype world model that bridges digital perception and biological computation. Bio-WM combines a CNN encoder with a simulated DishBrain-inspired spiking neural network (LIF neurons, S…

    Python 1

  2. GenomicSophia GenomicSophia Public

    KAIROS · Patient Scoring Dashboard AI-assisted genomic case triage — built for the SOPHiA Genetics × ETH Zurich Future of Health Hackathon (May 8–10, 2026). Helps genomic pathologists prioritize th…

    Python 3

  3. hack2026-dimos-slamass hack2026-dimos-slamass Public

    Forked from sherifnafie/dimos-slamass

    What happens when you give a robot autonomy, memory, and language? At #HACK2026 organized by ETH Robotic Club, we spent 48 hours building an answer. Working on the Unitree Go2 from Unitree Robotics…

    Python

  4. GenomicOracle GenomicOracle Public

    GenomicOracle is a web-based genomic analysis platform built for the AI for Health Hackathon. It combines Quantum Machine Learning (via PennyLane), LLM-powered clinical reasoning (Gemini / OpenAI /…

    Python 1

  5. RL-HumanoidControlPPO RL-HumanoidControlPPO Public

    This repository features an implementation of the PPO algorithm to solve the Humanoid-v5 high-dimensional control task. It leverages Stable-Baselines3 and Gymnasium for training and visualizing a r…

    Python

  6. psview-agent-simulator psview-agent-simulator Public

    Autonomous AI recruiter agent that self-configures from company context, generates personalized outreach sequences, and runs candidate conversations with a visible multi-step reasoning loop. Suppor…

    TypeScript 1