Data Science Seminars@Ciências

Biclustering in Biomedical Data Analysis: Algorithms and Applications

Sala 6.3.38, FCUL, Lisboa

Biclustering, the discovery of sets of objects with coherent values/patterns on subsets of features, was shown to be key to unravel and characterize informative regions (biclusters) within matricial, time series and network data, in a wide-set of applications in biomedical and social data analysis. Particularly in biomedical problems, where groups of genes or patients tend to be only meaningfully related on a subset of the sampled/monitored conditions. The challenging combinatorial nature of the biclustering problem led to the development of several approaches with variations on the allowed type, number, positioning and quality of biclusters. The state of the art relies on efficient string processing and mining techniques, in the case of biclustering temporal data, and pattern mining algorithms, in the general case of biclustering matricial and network data.

This talk introduces the biclustering problem comparing it to the traditional clustering problem, provides an overview on state of the art on biclustering  matricial and network data analysis, and then focus the problem of biclustering temporal data, tackling in particular the problem of biclustering gene expression time series obtained from transcriptomics. On going work on new triclustering algorithms to simultaneouly analyse multiple gene expression time series (three-way time series) and multiple multivariate time series collected at clinical follow-up, together with their applications in biomedical problems, such as the identification of disease progression patterns in the NEUROCLINOMICS2 project (PTDC/EEI-SII/1937/2014), are discussed.  

Short Bio: SARA C. MADEIRA is an Associate Professor at the Department of Informatics of the Faculty of Sciences, University of Lisbon (FCUL), since mid February 2017, where she teaches graduate courses on data mining, machine learning and foundations of data science and an under-graduate course on intelligent systems. She is also a senior researcher at LASIGE, where she is a member of the Data and Systems Intelligence, and Health and Biomedical Informatics research lines. Her research interests include data mining, machine learning, bioinformatics and medical informatics. In this context, she was the PI of "NEUROCLINOMICS - Understanding NEUROdegenerative diseases through CLINical and OMICS data" (PTDC/EIA-EIA/111239/2009), a research project embracing the challenges of studying complex diseases and developing efficient and effective mining algorithms for biomedical data, using Amyotrophic Lateral Sclerosis and Alzheimer's disease as case studies, which was followed by the ongoing project "NEUROCLINOMICS2 - Unravelling Prognostic Markers in NEUROdegenerative diseases through CLINical and OMICS data integration" (PTDC/EEI-SII/1937/2014). Her survey on "Biclustering Algorithms for Biological Data Analysis" was considered an ESI Hot Paper in Computer Science in November 2006. Biclustering algorithms and their applications in biomedical data analysis are still her main research topics.

14h00
Departamento de Informática

Seminário do Laboratório de Instrumentação e Física Experimental de Partículas, por Pedro Cruz (Northeastern University).

Logótipo do EVM 2024

Por Giosuè Muratore (DM Ciências ULisboa e CMAFcIO).

Logótipo do EVM 2024

Por Pedro Duarte (DM Ciências ULisboa, CMAFcIO).

Título do programa, sobre mosaico de fotografias de jovens cientistas

As candidaturas encontram-se encerradas. Obrigada aos quase 80 candidatos/as!

Fotografia de ilha

Seminários Doutorais no âmbito da disciplina de Projeto de Investigação (Doutoramento em Ciências do Mar).

Logótipo do EVM 2024

Por Maria Manuel Torres (DM Ciências ULisboa e CMAFcIO).

Seminário do Centro de Matemática, Aplicações Fundamentais e Investigação Operacional, por Baptiste Claustre (aluno ENS Lyon, estagiário CMAFcIO).

Logótipo do EVM 2024

Por: Jorge Buescu (DM Ciências ULisboa e CMAFcIO).

Titulo e data do evento, com imagem de ponte sobre o tejo

Um evento organizado no âmbito da Ação COST EURO-MIC, de cujo Comitê de Gestão Elisabete Silva, líder do Bioactive and Multifunctional Materials Lab do BioISI, faz parte.

Logótipo do EVM 2024

Por Jean-Baptiste Casteras (DM Ciências ULisboa e CMAFcIO).

Chegou a hora: os participantes do Programa Ser Cientista vão apresentar os projetos que desenvolveram ao longo de uma semana, acompanhados por docentes e investigadores de CIÊNCIAS. E todos podem assistir!

Imagem do evento

Extended enrolement date until July 12th.

Logótipo do evento, sobre um fundo branco

Um evento de reunião da comunidade nacional nas diversas vertentes da informática, com a ambição de ser o fórum de eleição para a divulgação, discussão e reconhecimento de trabalhos científicos.

Are you ready for this year's edition?

Imagem do evento - título, local e data do evento

Investigação Ecológica ao Serviço da Conservação

A leading venue for presenting and discussing the latest research, industrial practice and innovations in dependable and secure computing.