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Pages

Posts

GIT: New web-site in progress - UPDATE

less than 1 minute read

Published:

I decided to revamp my website with something that was more easily manageble. Talking with collegues I decided to give Jekyll a try. Setting the site up is taking longer than I thought, but I am slowly getting there. Hopefully this winter break will be helpful. Stay tuned!

GIT: Social Network Analysis for the network scientist

3 minute read

Published:

Since I moved to IUNI as an Assistant Research Scientist, I have been struggling to communicate in a precise scientific language with network scientist in Sociology. The main problem being that the same terms I have learned from network scientists in Informatics do not always mean exactly the same thing in the two disciplines.
So here I am going to try and put together a list of resources for Informatics/Physics trained network scientist to better navigate the long history of Social Network Analysis in Sociology.

GIT: New pre-print on BioArxiv

less than 1 minute read

Published:

New work out, together with collaborators at King’s College London, Imperial College London and ISI Foundation. We applied the Mapper algorithm to the AHBA (Allen Human Brain Atlas). Our results suggest that topological network descriptions can be a powerful tool to explore the relationships between genetic pathways and their association with brain function and its perturbation due to illness and/or pharmacological challenge.

code

S.A.S.S.A.F.R.A.S.

A small script that looks for unread Google Scholar Alerts emails in your Gmail account and saves each paper in a Google Spreadsheet as:
Title/ Authors - Journal/ Google Scholar link/ Date/ number of Alerts that contained the paper

TDA summary for gene-expression: Mapper Algorithm in 2D

Code for reproducing results in the paper “Topological gene-expression networks recapitulate brain anatomy and function”.
We present a pipeline based on the Mapper algorithm, a topological simplification tool, to produce and analyze genes co-expression data.
The code contains an implementation of the Mapper algorithm with 2 filters and to compute the agreement edge density matrices for the optimal parameters.

portfolio

publications

GIT: Complex politics: A quantitative semantic and topological analysis of uk house of commons debates.

Gurciullo, S., Smallegan, M., Pereda, M., Battiston, F., Patania, A., Poledna, S., ... & Mikhaylov, S. (2015). "Complex politics: A quantitative semantic and topological analysis of uk house of commons debates." arXiv preprint. arXiv:1510.03797. arXiv:1510.03797., 2015

An exploratory attempt to use quantitative semantics techniques and topological analysis to analyze systemic patterns arising in a complex political system.

GIT: Topological analysis of data

Patania, A., Vaccarino, F., & Petri, G. (2017). "Topological analysis of data." EPJ Data Science. 6(1), 7. EPJ Data Science, 2017

An editorial where we briefly present the TDA paradigm and some applications, in order to highlight its relevance to the data science community.

GIT: The shape of collaborations.

Patania, A., Petri, G., & Vaccarino, F. (2017). "The shape of collaborations." EPJ Data Science. 6(1), 18. EPJ Data Science, 2017

A study on the structure of scientific collaborations using simplicial descriptions of publications. We extend the concept of triadic closure to simplicial complexes and introduce a new way of dealing with large simplex sizes when computing homology.

GIT: Topological gene-expression networks recapitulate brain anatomy and function.

Patania, A., Selvaggi, P., Veronese, M., DiPasquale, O., Expert, P., & Petri, G. (2018). "Topological gene-expression networks recapitulate brain anatomy and function." arXiv preprint. bioRxiv, 476382. bioRxiv, 476382, 2018

We present a pipeline based on Mapper to analyze genes co-expression data. We find that co-expression networks produced by Mapper returned a structure that matches the well-known anatomy of the dopaminergic pathway.

talks

teaching

GIT: Teaching experience 1

Undergraduate course, University 1, Department, 2014

This is a description of a teaching experience. You can use markdown like any other post.

GIT: Teaching experience 2

Workshop, University 1, Department, 2015

This is a description of a teaching experience. You can use markdown like any other post.