About
Scientist & AI Specialist
- CV: [PDF]
- Website: jmtomczak.github.io
- Email: jmk.tomczakgmail.com
- City: Amsterdam, the Netherlands
Jakub M. Tomczak is an assistant professor of Artificial Intelligence in the Computational Intelligence group (led by Prof. A.E. Eiben) at Vrije Universiteit Amsterdam. Before joining Vrije Universiteit Amsterdam, he was a deep learning researcher (Engineer, Staff) in Qualcomm AI Research in Amsterdam, a Marie Sklodowska-Curie individual fellow in Prof. Max Welling's group at the University of Amsterdam, and an assistant professor and postdoc at the Wroclaw University of Technology. His main research interests include deep generative modeling, deep learning, and Bayesian inference, with applications to image processing, robotics, and life sciences. He is the author of the book entitled "Deep Generative Modeling". He is also the founder of Amsterdam AI Solutions.
Facts
Years of Experience
Supervised projects
Top publications
Funding gathered (EUR)
Additional Information
Presentations
My presentations at conferences, workshops, for academic and industrial research groups, summer schools
DeeBMed
My project that was carried out from 2016/10/1 to 2018/09/30 within the Marie Skłodowska-Curie Action (Individual Fellowship), financed by the European Comission.
My Book
My book on Generative Artificial Intelligence. This is the first comprehensive book on deep generative modeling explaining theory behind Diffusion-based models, Variational Auto-Encoders, GANs, autoregressive models, flow-based models, and energy-based models. Moreover, each chapter is associated with code snippets presenting how the beforementioned models could be implemented in PyTorch.
Resume
Education
Ph.D. in Computer Science/Machine Learning (with honors)
Mar 2013
Wroclaw University of Technology, Poland
Title: Incremental Knowledge Extraction from Data for Non-Stationary Objects
Supervisor: Prof. Jerzy Swiatek
M.Sc. in Computer Science
Dec 2009
Blekinge Institute of Technology, Sweden
M.Sc. in Computer Science (the best thesis in Poland)
Jul 2009
Wroclaw University of Technology, Poland
Work Experience
Advisor
Mar 2022 - Present
NatInLab, Amsterdam, the Netherlands
Assistant Professor of Artificial Intelligence
Nov 2019 - present
Vrije Unviersiteit Amsterdam, the Netherlands
Deep Learning Researcher (Staff Engineer)
Oct 2018 - Dec 2019
Qualcomm AI Research, Amsterdam, the Netherlands
Postdoc/Marie Sklodowska-Curie Individual Fellow
Oct 2016 - Sept 2018
Universiteit van Amsterdam, the Netherlands
Researcher (part-time)
Feb 2016 - Jun 2016
INDATA SA, Wroclaw. Poland
Assistant Professor
Oct 2014 - Sept 2016
Wroclaw University of Technology. Poland
Postdoc
Oct 2012 - Sept 2014
Wroclaw University of Technology. Poland
Ph.D. student / Research assistant
Jun 2009 - Sept 2012
Wroclaw University of Technology. Poland
Publications
Book
J.M. Tomczak, ''Deep Generative Modeling'', Springer, Cham, 2022.
Conference Papers
A. Kuzina, M. Welling„ J.M. Tomczak, On Alleviating Adversarial Attacks on Variational Autoencoders with MCMC, NeurIPS 2022
K. Deja, A. Kuzina, T. Trzcinski, J.M. Tomczak, On Analyzing Generative and Denoising Capabilities of Diffusion-based Deep Generative Models, NeurIPS 2022
D.W. Romero, R.-J. Bruintjes, J.M. Tomczak, E.J. Bekkers, M. Hoogendoorn, J. van Gemert, Flexconv: Continuous kernel convolutions with differentiable kernel sizes, ICLR, 2022
D.W. Romero, A. Kuzina, E.J. Bekkers, J.M. Tomczak, M. Hoogendoorn, CKCONV: Continuous kernel convolution for sequential data, ICLR, 2022
E. Krieken, J.M. Tomczak, A. ten Teije, Storchastic: A Framework for General Stochastic Automatic Differentiation, NeurIPS, 2021
Y. Perugachi-Diaz, J.M. Tomczak, S. Bhulai, Invertible DenseNets with concatenated Lipswish, NeurIPS, 2021
M. Ilse, J.M. Tomczak, P. Forre, Selecting data augmentation for simulating interventions, ICML 2021
D.W. Romero, E.J. Bekkers, J.M. Tomczak, M. Hoogendoorn, Attentive group equivariant convolutional networks, ICML 2020
E. Hoogeboom, V. Garcia Satorras, J.M. Tomczak, M. Welling, The convolution exponential and generalized sylvester flows, NeurIPS 2020
J.M. Tomczak, E. Weglarz-Tomczak, A.E. Eiben, Differential evolution with reversible linear transformations, GECCO 2020
M. Ilse, J.M. Tomczak, C. Louizos, M. Welling, DIVA: Domain invariant variational autoencoders, MIDL 2020
D. Abati, J.M. Tomczak, T. Blankevoort, S. Calderara, R. Cucchiara, B. Ehteshami Bejnordi, Conditional Channel Gated Networks for Task-Aware Continual Learning, CVPR, 2020
I. Gatopoulos, R. Lepert, A. Wiggers, G. Mariani, J.M. Tomczak, Evolutionary Algorithm with Non-parametric Surrogate Model for Tensor Program Optimization, IEEE CEC 2020
CY. Oh, J.M. Tomczak, E. Gavves, M. Welling, Combinatorial Bayesian Optimization using the Graph Cartesian Product, NeurIPS, Vancouver, Canada, 2019
A. Habibian, T. van Rozendaal, J.M. Tomczak, T.S. Cohen, Video compression with rate-distortion autoencoders, ICCV, Seol, South Korea, 2019
T. Davidson, L. Falorsi, N. de Cao, T. Kipf, J.M. Tomczak, Hyperspherical Variational Auto-Encoders, UAI, Monterey, California, the USA, 2018
R. van den Berg, L. Hasenclever, J.M. Tomczak, M. Welling, Sylvester Normalizing Flow for Variational Inference, UAI, Monterey, California, the USA, 2018
M. Ilse*, J.M. Tomczak*, M. Welling, Attention-based Deep Multiple Instance Learning, ICML, Stockholm, Sweden, 2018
J.M. Tomczak, M. Welling, VAE with a VampPrior, AISTATS, the Canary Islands, 2018
J.M. Tomczak, M. Welling, Improving Variational Auto-Encoders using convex combination linear Inverse Autoregressive Flow, Benelearn 2017, Eindhoven, the NL, 2017
J.M. Tomczak, M.Welling, Improving Variational Auto-Encoders using Householder Flow, NIPS Workshop on Bayesian Deep Learning, Barcelona, Spain, 2016
Journal articles
J. Luo, A. Stuurman, J.M. Tomczak, J. Ellers, A.E. Eiben, The Effects of Learning in Morphologically Evolving Robot Systems, Frontiers in Robotics and AI, 2022
G. Lan, J.M. Tomczak, D.M. Roijers, A.E. Eiben., Time efficiency in optimization with a bayesian-evolutionary algorithm, Swarm and Evolutionary Computation, 2022
F. Lavitt, D.J. Rijlaarsdam, D. van der Linden, E. Weglarz-Tomczak, J.M.Tomczak, Deep learning and transfer learning for automatic cell counting in microscope images of human cancer cell lines, Applied Sciences, 2021
G. Lan, M. van Hooft, M. De Carlo, J.M.Tomczak, A.E. Eiben, Learning locomotion skills in evolvable robots, Neurocomputing, 2021 \item Y. Perugachi-Diaz, J.M. Tomczak, S. Bhulai, Deep learning for white cabbage seedling prediction, Computers and Electronics in Agriculture, 2021
E. Weglarz-Tomczak, J.M. Tomczak, M. Talma, M. Burda-Grabowska, M. Giurg, S. Brul, Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2, Scientific Reports, 2021
I.A. Auzina, J.M. Tomczak, Approximate bayesian computation for discrete spaces, Entropy, 2021
I. Gatopoulos, J.M. Tomczak, Self-supervised variational auto-encoders, Entropy, 2021
E. Weglarz-Tomczak, J.M. Tomczak, S. Brul, M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models, Bioinformatics, 2021
E. Weglarz-Tomczak, D.J. Rijlaarsdam, J.M. Tomczak, S. Brul, GEM-based metabolic profiling for Human Bone Osteosarcoma under different glucose and glutamine availability, International Journal of Molecular Sciences 22 (3), 1470, 2021
E. Weglarz-Tomczak, J.M. Tomczak, A.E. Eiben, S. Brul, Population-Based Parameter Identification for Dynamical Models of Biological Networks with an Application to Saccharomyces cerevisiae, Processes 9 (1), 98, 2021
J.M. Tomczak, E. Weglarz-Tomczak, Estimating kinetic constants in the Michaelis‐Menten model from one enzymatic assay using Approximate Bayesian Computation, FEBS Letters, 2019
J.M. Tomczak, S. Zareba, S. Ravanbakhsh, R. Greiner, Low-Dimensional Perturb-and-MAP Approach for Learning Restricted Boltzmann Machines, Neural Processing Letters, 2017
M. Drewniak, E. Weglarz-Tomczak, K. Ozga, E. Rudzinska-Szostak, K. Macegoniuk, J.M. Tomczak, M. Bejger, W. Rypniewski, L. Berlicki, Helix-loop-helix peptide foldamers and their use in the construction of hydrolase mimetics, Bioorganic Chemistry, Vol. 81, pp. 356--361
A. Gonczarek, J.M. Tomczak, S. Zareba, J. Kaczmar, P. Dabrowski, M. Walczak, Interaction prediction in structure-based virtual screening using deep learning, Computers in Biology and Medicine, 2017
M. Zieba, S. Tomczak, J.M. Tomczak, Ensemble Boosted Trees with Synthetic Features Generation in Application to Bankruptcy Prediction, Expert Systems with Applications, Vol. 58, pp. 593--101, 2016
J.M. Tomczak, On some properties of the low-dimensional Gumbel perturbations in the Perturb-and-MAP model, Statistics and Probability Letters, 2016
J.M. Tomczak, A. Gonczarek, Learning invariant features using Subspace Restricted Boltzmann Machine, Neural Processing Letters, 2016
A. Gonczarek, J.M. Tomczak, Articulated tracking with manifold regularized particle filter, Machine Vision and Applications, Volume 27, Issue 2, pp 275--286
J.M. Tomczak, Learning Informative Features from Restricted Boltzmann Machines, Neural Processing Letters
J.M. Tomczak, M. Zieba, Probabilistic combination of classification rules and its application to medical diagnosis, Machine Learning, Vol. 101, Issue 1, pp. 105-135
J.M. Tomczak, M. Zieba, Classification Restricted Boltzmann Machine for comprehensible credit scoring model, Expert Systems with Applications, Volume 42, Issue 4, March 2015
M. Zieba, J.M. Tomczak, Boosted SVM with active learning strategy for imbalanced data, Soft Computing, August 2014, Pages 99--108
M. Zieba, J.M. Tomczak, J. Swiatek, M. Lubicz, Boosted SVM for extracting rules from imbalanced data in application to prediction of the post-operative life expectancy in the lung cancer patients, Applied Soft Computing, Volume 14, Part A, January 2014, Pages 99--108
J.M. Tomczak, A. Gonczarek, Decision rules extraction from data stream in the presence of changing context for diabetes treatment, Knowledge and Information Systems, 2013, Vol. 34, Issue 3, pp. 521--546
BLOG
- All
- VAEs
- GANs
- Flows
- ARMs
- Joint
- Theory
- Applications
Contact
Location:
De Boelelaan 1111, 1081 HV, Amsterdam, the Netherlands
Email:
jmk.tomczakgmail.com