On February 14, at 10:00, OLISSIPO project will host an online talk (live transmission) by Prof. Jonas Almeida, Senior investigator and Data Science director at the National Cancer Institute. The talk is titled “Universal Sequence Maps, from biological sequences to numbers and back”.
Date & Time: January 14, 10:00 – 11:00
Where: Online via Zoom (
here), or INESC – ID (live transmission), Rua Alves Redol, 9, 1000-029 Lisboa | Room 336
Abstract: Universal Sequence Maps (USM) are an iterated mapping technique that can represent sequence succession in a manner that is both bijective and scale-free. In its original unidirectional form, proposed in 1990 as Chaos Game Representation (CGR), it was proposed as a graphical representation of gene structure that borrowed methodologically from statistical mechanics of complex dynamic phenomena. Over a decade later, CGR was found to provide an alignment-free route to sequence analysis that generalizes Markovian succession. In the subsequent 2 decades, new properties were uncovered and the iterated technique was reformulated, as reviewed in this presentation. Intriguingly, the modern bidirectionally iterated form, USM, appears to offer a convenient route to develop language models of Biological sequences for generative AI applications.
Bio: Prof. Jonas Almeida holds the position of (tenured) Senior investigator and Data Science director at the National Cancer Institute, Division of Cancer Epidemiology and Genetics (NIH/NCI intramural program). He also maintains academic positions at the State University of New York (SUNY – Stony Brook), Queen’s University Belfast, UK, and George Mason University in Virginia. He started his academic career at the University of Lisbon (PhD Biological Engineering, 1995), where he remains involved in collaborative initiatives towards Artificial intelligence, Cloud Computing, and the development of consumer-facing polygenic risk calculators for Precision Prevention. For the list of publications and a more granular biosketch see jonasalmeida.info.
