Dr. Dmitry Kobak

Dmitry Kobak
Dmitry Kobak is a group leader in the Department of Data Science at the Hertie Institute for AI in Brain Health at the University of Tübingen. He is interested in unsupervised and self-supervised learning, in particular contrastive learning, manifold learning, and dimensionality reduction for two-dimensional visualization of high-dimensional biological datasets such as single-cell transcriptomic datasets. He has also worked on statistical forensics and has been involved in the analysis of Russian electoral falsifications and Covid-19 excess mortality. He is a member of the ELLIS society and an IMPRS-IS associated scientist.
Unsupervised data exploration plays an important role in many areas of science and becomes increasingly crucial as collected datasets grow in size and complexity.
01
Lause, J., Berens, P., Kobak, D.

The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense

Oct 02, 2024 | Computation Biology
02
González-Márquez, R., Schmidt, L., Schmidt, B. M., Berens, P., & Kobak, D.

The landscape of biomedical research

Apr 09, 2024 | Patterns, 100968
03
Böhm, J. N., Berens, P., & Kobak, D.

Unsupervised visualization of image datasets using contrastive learning

May 30, 2023 | Proceedings of the International Conference on Learning Representations (ICLR)
04
Damrich, S., Böhm, J. N., Hamprecht, F. A., & Kobak, D.

From t-SNE to UMAP with contrastive learning

May 30, 2023 | Proceedings of the International Conference on Learning Representations (ICLR)
05
Bachmann, F., Hennig, P., Kobak, D.

Wasserstein tSNE

Mar 17, 2023 | European Conference on Machine Learning 2023
06
Shen, S., Jiang, X., Scala, F., Fu, J., Fahey, P., Kobak, D., ... & Tolias, A. S.

Distinct organization of two cortico-cortical feedback pathways.

Oct 27, 2022 | Nature Communications, 2022, 13. Jg., Nr. 1, S. 6389.
07
Bashford, L., Kobak, D., Diedrichsen, J., & Mehring, C.

Motor skill learning decreases movement variability and increases planning horizon.

Apr 04, 2022 | Journal of Neurophysiology, 127(4), 995-1006.
08
Böhm, J. N., Berens, P., & Kobak, D.

Attraction-repulsion spectrum in neighbor embeddings

Feb 21, 2022 | The Journal of Machine Learning Research, 23(1), 95, 4118–4149
09
Scala, F., Kobak, D., Bernabucci, M., Bernaerts, Y., Cadwell, C. R., Castro, J. R., [...], Berens, P. & Tolias, A. S.

Phenotypic variation of transcriptomic cell types in mouse motor cortex

Oct 07, 2021 | Nature, 598(7879), 144-150
10
Ilanchezian, I., Kobak, D., Faber, H., Ziemssen, F., Berens, P., & Ayhan, M. S

Interpretable gender classification from retinal fundus images using BagNets.

Sep 21, 2021 | Proceedings, Part III 24 (pp. 477-487). Springer International Publishing.
11
Lause, J., Berens, P., & Kobak, D.

Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data.

Sep 09, 2021 | Genome biology, 22(1), 1-20
12
Kobak, D., Bernaerts, Y., Weis, M. A., Scala, F., Tolias, A. S., & Berens, P.

Sparse reduced-rank regression for exploratory visualisation of paired multivariate data

Aug 07, 2021 | Journal of the Royal Statistical Society Series C: Applied Statistics, 70(4), 980-1000
14
Kobak, D., & Linderman, G. C.

Initialization is critical for preserving global data structure in both t-SNE and UMAP

Feb 01, 2021 | Nature biotechnology, 39(2), 156-157.
15
Kobak, D., & Berens, P.

The art of using t-SNE for single-cell transcriptomics.

Nov 28, 2019 | Nature communications, 10(1), 5416.
16
Kobak, D., Linderman, G., Steinerberger, S., Kluger, Y., & Berens, P.

Heavy-tailed kernels reveal a finer cluster structure in t-SNE visualisations.

Sep 16, 2019 | Joint European Conference on Machine Learning and Knowledge Discovery in Databases. Cham: Springer International Publishing, 2019.
17
Scala, F., Kobak, D., Shan, S., Bernaerts, Y., Laturnus, S., Cadwell, C. R., ... Berens, P., ... & Tolias, A. S

Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas

Sep 13, 2019 | Nature communications, 10(1), 4174.