Publications

Curated research outputs from the MLKD group.

all types Journal Conference Book / Chapter Preprint

2026

Dynamic feature selection improves influenza forecasting accuracy and generalization across countries

Jingyi Liang, Zhiqi Zeng, Kai Liao, Min Liao, Zhonghao Fang, Lesi Kong, Jianlin Feng, Na Yu, Zhengshi Lin, Chitin Hon, Arlindo L. Oliveira, Zifeng Yang

Journal of Advanced Research journal summary

2025

Non-invasive derivation of instantaneous free-wave ratio from invasive coronary angiography using a new deep learning artificial intelligence model and comparison with human operators’ performance

Catarina Oliveira, Marta Vilela, João Silva Marques, Cláudia Jorge, Tiago Rodrigues, Ana Rita Francisco, Rita Marante de Oliveira, Beatríz Silva, João Lourenço Silva, Arlindo L. Oliveira, Fausto J. Pinto, Miguel Nobre Menezes

The International Journal of Cardiovascular Imaging journal

Pre-trained VGG16 model for forensic dental age estimation

Valon Nushi, Rui Santos, Hrvoje Brkić, Arlindo L. Oliveira, Alexandre P. Francisco, Cristiana Palmela Pereira

Egyptian Journal of Forensic Sciences journal

Enhancing the Interpretation of Spirometry: Joint Utilization of n-Order Adaptive Fourier Decomposition and Deep Learning Techniques

Xuanfeng Li, Yuxi Lin, Wei He, Ruibin Liu, Arlindo L. Oliveira, Tao Qian, Jinping Zheng, Chi Tin Hon

IEEE Transactions on Instrumentation and Measurement journal

2024

Contribution of V1 Receptive Field Properties to Corruption Robustness in CNNs

Ruxandra Bărbulescu, Tiago Marques, Arlindo L. Oliveira

Frontiers in artificial intelligence and applications journal

Adaptive Fourier Decomposition of the First Three SARS-CoV-2 Infection Waves with Epidemic Intervention — London, UK, 2020–2022

Zige Liu, Guibin Lu, Cheokieng Vong, Zhiqi Zeng, Wei He, Zhijie Lin, Cuiyun Lin, Kaichin Hsieh, Zifeng Yang, Arlindo L. Oliveira, Chitin Hon, Queen Ethelburga’s Collegiate, Thorpe Underwood Estate, York, UK, Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento em Lisboa, Lisboa, Portugal

China CDC Weekly journal

Old Habits Die Hard

Miguel Nobre Menezes, Catarina Oliveira, João Lourenço Silva, Beatriz Valente Silva, João Silva Marques, Cláudio Guerreiro, J Guedes, Manuel Oliveira‐Santos, Arlindo L. Oliveira, Fausto J. Pinto

JACC Advances journal

Coronary Physiology Instantaneous Wave-Free Ratio (iFR) Derived From X-Ray Angiography Using Artificial Intelligence Deep Learning Models: A Pilot Study

Miguel Nobre Menezes, João Lourenço Silva, Beatriz Silva, Rita Marante de Oliveira, Tiago Rodrigues, Arlindo L. Oliveira, Fausto J. Pinto

The Journal of invasive cardiology/The journal of invasive cardiology journal

Multiple Instance Learning for WSI: A comparative analysis of attention-based approaches

Martim Afonso, Praphulla Bhawsar, Monjoy Saha, Jonas S. Almeida, Arlindo L. Oliveira

Journal of Pathology Informatics journal

Training environmental sound classification models for real-world deployment in edge devices

Manuel Goulão, L. Bandeira, Bruno Martins, Arlindo L. Oliveira

Discover Applied Sciences journal

2023

Development of a machine learning model using 12-lead ECG to improve acute dianosis of pulmonary embolism

B V Silva, João Silva Marques, Miguel Nobre Menezes, Arlindo L. Oliveira, Fausto J. Pinto

European Heart Journal journal

Potential and limitations of computed tomography images as predictors of the outcome of ischemic stroke events: a review

Gonçalo Oliveira, Ana Catarina Fonseca, José M. Ferro, Arlindo L. Oliveira

Frontiers in Stroke journal

Pretraining the Vision Transformer Using Self-Supervised Methods for Vision Based Deep Reinforcement Learning

Manuel Goulão, Arlindo L. Oliveira

Frontiers in artificial intelligence and applications journal

Temporary impact on medical system and effectiveness of mitigation strategies after COVID-19 policy adjustment in China: a modeling study

Chitin Hon, Jingyi Liang, Ruihan Chen, Zhijie Lin, Yangqianxi Wang, Wei He, Ruibin Liu, Jiaxi Sun, Qianyin Li, Lixi Liang, Minyi Zhang, Zichen Chang, Yinqiu Guo, Wenting Zeng, Tie Liu, Arlindo L. Oliveira

Frontiers in Public Health journal

Segmentation of X‐ray coronary angiography with an artificial intelligence deep learning model: Impact in operator visual assessment of coronary stenosis severity

Miguel Nobre Menezes, Beatríz Silva, João Lourenço Silva, Tiago Rodrigues, João Silva Marques, Cláudio Guerreiro, J Guedes, Manuel Oliveira‐Santos, Arlindo L. Oliveira, Fausto J. Pinto

Catheterization and Cardiovascular Interventions journal

Deep Learning-Based Extraction of Biomarkers for the Prediction of the Functional Outcome of Ischemic Stroke Patients

Gonçalo Oliveira, Ana Catarina Fonseca, José M. Ferro, Arlindo L. Oliveira

Diagnostics journal

Learning the dynamics of realistic models of C. elegans nervous system with recurrent neural networks

Ruxandra Bărbulescu, Gonçalo Mestre, Arlindo L. Oliveira, L. Miguel Silveira

Scientific Reports journal

Coronary X-ray angiography segmentation using Artificial Intelligence: a multicentric validation study of a deep learning model

Miguel Nobre Menezes, João Lourenço Silva, Beatríz Silva, Tiago Rodrigues, Cláudio Guerreiro, J Guedes, Manuel Oliveira‐Santos, Arlindo L. Oliveira, Fausto J. Pinto

The International Journal of Cardiovascular Imaging journal

Artificial intelligence-based diagnosis of acute pulmonary embolism: Development of a machine learning model using 12-lead electrocardiogram

Beatriz Valente Silva, João Marques, Miguel Nobre Menezes, Arlindo L. Oliveira, Fausto J. Pinto

Revista Portuguesa de Cardiologia journal

2022

A blueprint for conscious machines

Arlindo L. Oliveira

Proceedings of the National Academy of Sciences journal

Modeling the Geospatial Evolution of COVID-19 using Spatio-temporal Convolutional Sequence-to-sequence Neural Networks

Mário Cardoso, André Cavalheiro, Alexandre Borges, Ana Filipa Duarte, A. Soares, Maria João Veloso da Costa Ramos Pereira, Nuno Nunes, Leonardo Azevedo, Arlindo L. Oliveira

ACM Transactions on Spatial Algorithms and Systems journal

Development of deep learning segmentation models for coronary X-ray angiography: Quality assessment by a new global segmentation score and comparison with human performance

Miguel Nobre Menezes, João Lourenço-Silva, Beatriz Silva, Tiago Rodrigues, Ana Rita Francisco, Pedro Santos Ferreira, Arlindo L. Oliveira, Fausto J. Pinto

Revista Portuguesa de Cardiologia journal

2020

Graph Neural Networks for Traffic Forecasting

João Rico, José Barateiro, Arlindo L. Oliveira

OMAINTEC journal. journal

2019

The bio.tools registry of software tools and data resources for the life sciences

Jon Ison, Hans Ienasescu, Piotr Jaroslaw Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo López, Séverine Duvaud, Heinz Stockinger, Bertil Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiřı́ Vondrášek, Hedi Peterson, Ahto Salumets, Inge Jonassen, Rob Hooft, Tommi Nyrönen, Alfonso Valencia, Salvador Capella-Gutiérrez, Josep Lluis Gelpí, Federico Zambelli, Babis Savakis, Brane Leskošek, Kristoffer Rapacki, Christophe Blanchet, Rafael C. Jiménez, Arlindo L. Oliveira, Gert Vriend, Olivier Collin, Jacques van Helden, Peter Løngreen, Søren Brunak

Genome biology journal

Biotechnology, Big Data and Artificial Intelligence

Arlindo L. Oliveira

Biotechnology Journal journal

2018

Making algorithms work for us

Arlindo L. Oliveira

Nature Electronics journal

Computational Approach to the Discovery of Phytochemical Molecules with Therapeutic Potential Targets to the PKCZ protein

Poliany Graziella de Freitas, Thiago C. Elias, Icaro Alves Pinto, Luciano T. Costa, Paulo Vinícius Sanches Daltro de Carvalho, Daniel de Queiroz Omote, Ihosvany Camps, Tati Ishikawa, Helen Andrade Arcuri, Susana Vinga, Arlindo L. Oliveira, Walter Filgueira de Azevedo, Nelson José Freitas da Silveira

Letters in Drug Design & Discovery journal

Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients

Miguel Monteiro, Ana Catarina Fonseca, Ana T. Freitas, Teresa Pinho e Melo, Alexandre P. Francisco, José M. Ferro, Arlindo L. Oliveira

IEEE/ACM Transactions on Computational Biology and Bioinformatics journal

ISLES 2016 and 2017-Benchmarking Ischemic Stroke Lesion Outcome Prediction Based on Multispectral MRI

Stefan Winzeck, Arsany Hakim, Richard McKinley, José A. A. D. S. R. Pinto, Victor Alves, Carlos A. Silva, Maxim Pisov, Egor Krivov, Mikhail Belyaev, Miguel Monteiro, Arlindo L. Oliveira, Youngwon Choi, Myunghee Cho Paik, Yongchan Kwon, Hanbyul Lee, Beom Joon Kim, Joong‐Ho Won, Mobarakol Islam, Hongliang Ren, David Robben, Paul Suetens, Enhao Gong, Yilin Niu, Junshen Xu, John M. Pauly, Christian Lucas, Mattias P. Heinrich‬, Luis Carlos Rivera Monroy, Laura Silvana Castillo, Laura Daza, Andrew Beers, Pablo Arbelaezs, Oskar Maier, Ken Chang, James M. Brown, Jayashree Kalpathy–Cramer, Greg Zaharchuk, Roland Wiest, Mauricio Reyes

Frontiers in Neurology journal

2016

The ELIXIR channel in F1000Research

Niklas Blomberg, Arlindo L. Oliveira, Barend Mons, Bengt Persson, Inge Jonassen

F1000Research journal

DegreeCox – a network-based regularization method for survival analysis

André Veríssimo, Arlindo L. Oliveira, Marie‐France Sagot, Susana Vinga

BMC Bioinformatics journal

2015

The ELIXIR channel in F1000Research

Niklas Blomberg, Arlindo L. Oliveira, Barend Mons, Bengt Persson, Inge Jonassen

F1000Research journal

2013

Using Information Interaction to Discover Epistatic Effects in Complex Diseases

Orlando Anunciação, Susana Vinga, Arlindo L. Oliveira

PLoS ONE journal

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation inSaccharomyces cerevisiae

Miguel C. Teixeira, Pedro T. Monteiro, Joana F. Guerreiro, Joana P. Gonçalves, Nuno P. Mira, Sandra C. dos Santos, Tânia R. Cabrito, Margarida Palma, Catarina Costa, Alexandre P. Francisco, Sara C. Madeira, Arlindo L. Oliveira, Ana Teresa Freitas, Isabel Sá‐Correia

Nucleic Acids Research journal

2012

TAPYR: An efficient high-throughput sequence aligner for re-sequencing applications

Francisco Fernandes, Paulo G. S. da Fonseca, Luís M. S.Russo, Arlindo L. Oliveira, Ana T. Freitas

EMBnet journal journal

2011

QUANTITATIVE MODELING OF THESACCHAROMYCES CEREVISIAEFLR1 REGULATORY NETWORK USING AN S-SYSTEM FORMALISM

Dulce Calçada, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira

Journal of Bioinformatics and Computational Biology journal

Mining query log graphs towards a query folksonomy

Alexandre P. Francisco, Ricardo Baeza‐Yates, Arlindo L. Oliveira

Concurrency and Computation Practice and Experience journal

GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge

Alexandra M. Carvalho, Arlindo L. Oliveira

Algorithms for Molecular Biology journal

Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae

Pedro T. Monteiro, Paulo Jorge Dias, Delphine Ropers, Arlindo L. Oliveira, I. Sá-Correia, Miguel C. Teixeira, Ana T. Freitas

IET Systems Biology journal

Efficient alignment of pyrosequencing reads for re-sequencing applications

Francisco Fernandes, Paulo GS da Fonseca, Luís M. S.Russo, Arlindo L. Oliveira, Ana T. Freitas

BMC Bioinformatics journal

TFRank: network-based prioritization of regulatory associations underlying transcriptional responses

Joana P. Gonçalves, Alexandre P. Francisco, Nuno P. Mira, Miguel C. Teixeira, Isabel Sá‐Correia, Arlindo L. Oliveira, Sara C. Madeira

Bioinformatics journal

Discriminative Learning of Bayesian Networks via Factorized Conditional Log-Likelihood

Alexandra M. Carvalho, Teemu Roos, Arlindo L. Oliveira, Petri Myllymäki

Työväentutkimus Vuosikirja journal

Fully compressed suffix trees

Luís M. S.Russo, Gonzalo Navarro, Arlindo L. Oliveira

ACM Transactions on Algorithms journal

2010

Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches

Miguel C. Teixeira, Paulo Jorge Dias, Pedro T. Monteiro, Adrien Sala, Arlindo L. Oliveira, Ana T. Freitas, Isabel Sá‐Correia

Molecular BioSystems journal

Haplotype Inference by Pure Parsimony: A Survey

Ana Graça, Inês Lynce, João Marques‐Silva, Arlindo L. Oliveira

Journal of Computational Biology journal

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

D. Abdulrehman, Pedro T. Monteiro, Miguel C. Teixeira, Nuno P. Mira, Artur B. Lourenço, Sandra C. dos Santos, Tânia R. Cabrito, Alexandre P. Francisco, Sara C. Madeira, R. S. Aires, Arlindo L. Oliveira, Isabel Sá‐Correia, Ana T. Freitas

Nucleic Acids Research journal

2009

CONSTANT TIME CLASH DETECTION IN PROTEIN FOLDING

Miguel Bugalho, Arlindo L. Oliveira

Journal of Bioinformatics and Computational Biology journal

Haplotype inference with pseudo-Boolean optimization

Ana Graça, João Marques‐Silva, Inês Lynce, Arlindo L. Oliveira

Annals of Operations Research journal

Approximate String Matching with Compressed Indexes

Luís M. S.Russo, Gonzalo Navarro, Arlindo L. Oliveira, Pedro Morales

Algorithms journal

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

Sara C. Madeira, Arlindo L. Oliveira

Algorithms for Molecular Biology journal