Optimal Computation of Avoided Words
Kings College –
The deviation of the observed frequency of a word w from its
expected frequency in a given sequence x is used to determine whether
or not the word is avoided. This concept is particularly useful in DNA
linguistic analysis. The value of the standard deviation of w, denoted by
std(w), effectively characterises the extent of a word by its edge contrast
in the context in which it occurs. A word w of length k > 2 is a ρ-avoided
word in x if std(w) ≤ ρ, for a given threshold ρ < 0. Notice that such a word may be completely absent from x. Hence computing all such words naïvely can be a very time-consuming procedure, in particular for large k. In this talk, we propose an O(n)-time and O(n)-space algorithm to compute all ρ-avoided words of length k in a given sequence x of length n over a fixed-sized alphabet. We also present a time-optimal O(σn)-time algorithm to compute all ρ-avoided words (of any length) in a sequence of length n over an integer alphabet of size σ.
Date: 2016-Jun-28 Time: 14:00:00 Room: 408
For more information:
- 21 31 00272
Research data repositories and tools for human genomics data sharing
Inform the human research community of the status and availability of BioData.pt Local EGA and discuss its need and usability challenges.
The European Genome-phenome Archive (EGA) is a repository for all sequence and genotype experiment types, including case-control, population, and family studies. The EGA will serve as a permanent archive that will archive several levels of data, including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters.
Responding to national regulations over human data sharing and other constraints, BioData.pt deploys and operates a Local EGA instance and tools that allow data discovery of genomic and phenoclinic data, following the GA4GH standard and international best practices.
This workshop aims at informing the human research community of the status and availability of BioData.pt Local EGA and discuss from several perspectives its need and usability challenges.
Further details and registration are available here.
OLISSIPO Summer School in Lisbon | Computational phylogenetics to analyse the evolution of cells and communities
We are happy to announce the OLISSIPO Summer School on Computational phylogenetics to analyse the evolution of cells and communities, which will be held in Lisbon, Portugal, at INESC-ID, between July 2-7, 2023.
David Posada, University of Vigo (class)
João Alves, University of Vigo (hands-on)
Nadia El-Mabrouk, Université de Montréal (class)
Mattéo Delabre, Université de Montréal (hands-on)
Ran Libeskind-Hadas, Claremont McKenna College (class and hands-on)
Russell Schwartz, Carnegie Mellon University (class and hands-on)
See the preliminary agenda at: https://olissipo.inesc-id.pt/tree-tango-school
Registration is mandatory. You can register at: https://forms.gle/VsASFHW5E7MJvaCc9
The registration fee is 250€ for students and OLISSIPO members and 350€ for postdocs or other researchers (meals indicated at the schedule of the school are included, accommodation and flights are not). All details will be made available upon registration.
We will have slots for flash talks (3-10 min depending on the number of submissions) to present yourself and the work you have been developing in your research.
The 13th Lisbon Machine Learning School | LxMLS 2023
The Lisbon Machine Learning Summer School (LxMLS) takes place yearly at Instituto Superior Técnico (IST). LxMLS 2023 will be a 6-day event (14-20 July, 2023), scheduled to take place as an in-person event.
The school covers a range of machine learning topics, from theory to practice, that are important in solving natural language processing problems arising in different application areas. It is organized jointly by Instituto Superior Técnico (IST), a leading Engineering and Science school in Portugal, the Instituto de Telecomunicações, the Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa (INESC-ID), the Lisbon ELLIS Unit for Learning and Intelligent Systems (LUMLIS), Unbabel, Zendesk, and IBM Research.
Check online for information about past editions: LxMLS 2011, LxMLS 2012, LxMLS 2013, LxMLS 2014, LxMLS 2015, LxMLS 2016, LxMLS 2017, LxMLS 2018, LxMLS 2019, LxMLS 2020, LxMLS 2021, LxMLS 2022 (you can also watch the videos of the lectures for 2016, 2017, 2018, and 2020).
31st International Conference on Information Systems Development (ISD 2023)
The 31st International Conference on Information Systems Development (ISD 2023) conference provides a forum for research and developments in the field of information systems. The theme of ISD 2023 is “Information systems development, organizational aspects and societal trends”. New trends in developing information systems emphasize the continuous collaboration between developers and operators in order to optimize the software delivery time. The conference promotes research on methodological and technological issues and how IS developers and operators are transforming organizations and society through information systems.
The ISD 2023 conference held this year also provides an opportunity for researchers and practitioners to promote their research, practical experience, and to discuss issues related to Information Systems through papers, posters, and journal-first paper presentations.
ISD 2023 will be hosted by Instituto Superior Técnico, in Lisbon, Portugal, on August 30–September 1, 2023.