Fatma Deniz

Who am I?

I am a Junior Group Leader and Principal Investigator at UC Berkeley and TU Berlin . I am interested in understanding how complex information is encoded in the brain and use machine-learning approaches to fit computational models to large-scale brain data acquired during natural tasks. Currently, I explore how more than one language can coexist in the human brain.

I was a postdoctoral researcher at the Helen Wills Neuroscience Institute in UC Berkeley, a Moore-and-Sloan Data Science Fellow at the Berkeley Institute for Data Science , and DAAD postdoctoral fellow at International Computer Science Institute (ICSI) in Berkeley. I did my Ph.D. in Computational Neuroscience at Bernstein Center for Computational Neuroscience in Berlin, obained a M.Sc. in Computer Science from the Technical University of Munich and worked at California Institute of Technology during my master’s thesis.

I routinely disregard disciplinary boundaries and follow my curiosity. This makes my work lie at the intersection between data science, neuroscience and artificial intelligence. I design and promote approaches for scientific reproducibility and co-edited a book on reproducibility published here. Here is an online version of the book. I also worked on improving online user authentication applications using image based authentication procedures combined with knowledge gained from cognitive neuroscience (Check MooneyAuth ) and created a database of two-tone Mooney images. E-mail me if you would like to use those for your research. Code is available on GitHub.

I am a passionate coder, baker, and I love feeling the resonance when I play the cello which makes me simply happy.

Here is my CV.

Publications

Book

Kitzes, J., Turek D., Deniz F., editors, The Practice of Reproducible Research: Case Studies in Data Science , UC Press, 2017. Online version book available at https://www.practicereproducibleresearch.org/.

Book Chapters

Deniz F., "pyMooney: Generating a Database of Two-Tone, Mooney Images ". In The Practice of Reproducible Research: Case Studies in Data Science. Kitzes, J., Turek D., Deniz F., editors. UC Press, 2017
Turek D., Deniz F., "Introducing the Case Studies". In The Practice of Reproducible Research: Case Studies in Data Science. Kitzes, J., Turek D., Deniz F., editors. UC Press, 2017

Journal and conference publications

Popham S., Huth A. G., Bilenko N. Y., Deniz F., Gao, S. J., Nunez-Elizalde A., Gallant J. L., Visual and linguistic semantic representations are aligned at the border of human visual cortex. Accepted in Nature Neuroscience. 2021
Ramakrishnan K. and Deniz F., Non-Complementarity of Information in Word-Embedding and Brain Representations in Distinguishing between Concrete and Abstract Words . In Proceedings of NAACL HLT Workshop on Cognitive Modeling and Computational Linguistics (CMCL), 2021
Deniz F., Nunez-Elizalde A.O., Huth A. G., Gallant J. L., The representation of semantic information across human cerebral cortex during listening versus reading is invariant to stimulus modality . Journal of Neuroscience, 39(39):7722-7736, 2019
Wu M.*, Deniz F.*, Prenger R., Gallant J. L., The unified maximum a posteriori (MAP) framework for neuronal system identification . (* First authorship shared), arXiv, https://arxiv.org/abs/1811.01043, 2018
Holdgraf C., Culich A., Rokem A., Deniz F., Ushuzima D., Alegro M., Portable learning environments for hands-on computational instruction: Using container- and cloud-based technology to teach data science . In Proceedings of the Practice and Experience in Advanced Research Computing on Sustainability, Success and Impact (p. 32), ACM, 2017
Castelluccia C., Duermuth M., Golla M., Deniz F.., MooneyAuth: Towards Practical Implicit Memory-based Authentication . In Network and Distributed System Security Symposium (NDSS), 2017
Kizilirmak J. M., Gomes da Silva J. G., Imamoglu F., Richardson-Klavehn A., Generation and the subjective feeling of "aha!": Independent contributions to learning from insight . Psychological research 80 (6), 1059-1074, 2015
Castelluccia C., Duermuth M., Imamoglu F., Learning from Neuroscience to Improve Internet Security . ERCIM News, Research and Innovation, 99:46, 2014
Imamoglu F., Heinzle J., Imfeld A., Haynes J.-D., Activity in high-level brain regions reflects visibility of low-level stimuli . Neuroimage, 102:688-694, 2014
Imamoglu F., Kahnt T., Koch C., Haynes J.-D., Changes in functional connectivity support conscious object recognition . Neuroimage, 63:1909-17, 2012

In preparation

Deniz F.*, Wehbe L.*, Tseng C.*, Gallant J.L., Different contextual effects modulate the representation of word meaning in the human brain (* First authorship shared)
Wehbe L., Huth A. G., Deniz F., Luise-Kieseler M., Gallant J. L., Automated simulation and replication of fMRI experiments
Bilenko N. Y, Deniz F., Huth A. G., Cukur T., Nishimoto S., de Heer W.A, Gallant J. L., FISCA: Functional Inter-Subject Component Analysis
Wehbe L., Nunez-Elizalde A., Huth A.G., Deniz F., Bilenko N., Gallant J. L., Deep multi-view representation learning of brain responses to natural stimuli