Publications

publications by categories in reversed chronological order (* equally contributed)

Mathematical foundations of AI

  • Alex Meterez * , Amir Joudaki * , Francesco Orabona, Alex Immer, Gunnar Ratsch, Hadi Daneshmand, “Batch normalization without gradient explosion: Towards training without depth limits”, Under review.
  • Amir Joudaki, Hadi Daneshmand, Francis Bach, “On the impact of activation and normalization in obtaining isometric embeddings at initialization”, NeurIPS 2023.
  • Amir Joudaki, Hadi Daneshmand, Francis Bach, “On Bridging the Gap between Mean Field and Finite Width in Deep Random Neural Networks with Batch Normalization”, ICML 2023.
  • Hadi Daneshmand, Amir Joudaki, Francis Bach, “Batch Normalization Orthogonalizes Representations in Deep Random Networks”, NeurIPS 2021 (spotlight, top 3% of submissiosn).
  • Alexandre Bense, Amir Joudaki, Tim G. J. Rudner, Vincent Fortuin, “PCA Subspaces Are Not Always Optimal for Bayesian Learning”, NeurIPS 2021 workshop (DistShift).

Genomics

  • Kacper Kapusniak, Manuel Burger, Gunnar Ratsch, Amir Joudaki, “Learning Genomic Sequence Representations using Graph Neural Networks over De Bruijn Graphs”, NeurIPS workshop 2023 (Graph Learning Frontiers).
  • Amir Joudaki * , Alexandru Meterez * , Harun Mustafa, Ragnar Groot Koerkamp, Andre Kahles, Gunnar Raetsch, “Aligning distant sequences to graphs using long seed sketches”, Journal of Genome Research 2023 (Cold Spring Harbor Laboratory press).
  • Amir Joudaki , Gunnar Ratsch, Andre Kahles, “Fast Alignment-Free Similarity Estimation By Tensor Sketching”, proceedings of RECOMB 2021.
  • Mikhail Karasikov, Harun Mustafa, Amir Joudaki , Sara Javadzadeh-No, Gunnar Rätsch, André Kahles, “Sparse Binary Relation Representations for Genome Graph”, Journal of computational biology: a journal of computational molecular cell biology 27.4 (2020): 626-639.

Dimensionality Reduction

  • Amir Najafi, Amir Joudaki , “Nonlinear Dimensionality Reduction via Path-Based Isometric Mapping”, IEEE transactions on pattern analysis and machine intelligence, 38(7), 1452-1464.

Neuroscience

  • Amir Joudaki , Elham Barzegaran, Mahdi Jalili*, Andrea O. Rossetti, Richard S. Frackowiak, and Maria G. Knyazeva, “Properties of functional brain networks affect frequency of psychogenic non-epileptic seizures”, Frontiers in Human Neuroscience, 6:335.
  • Amir Joudaki , Niloufar Salehi, Mahdi Jalili, Maria Knyazeva, “EEG-based functional brain networks: does the network size matter?”, PLoS ONE 7(4): e35673.