Fatma Deniz

Who am I?

I am a postdoctoral researcher in the Gallant lab in UC Berkeley. I am interested in how sensory information is encoded in the human brain and use machine learning approaches to fit computational models to large-scale functional neuroimaging data. Currently, using functional magnetic resonance imaging (fMRI) I try to understand how the brain represents and processes information when it performs a natural task. For example, when we listen to or read a story.

In addition, I design and promote approaches for scientific reproducibility. I 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.

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 Articles

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. J. Neurosci 2019, 10.1523/JNEUROSCI.0675-19.2019
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, 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

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)
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