Arlindo Oliveira

Arlindo Oliveira

Faculty

machine learning · bioinformatics · computational biology

LinkedIn ORCID Ciencia Vitae DBLP

Publications

2017

Arlindo L. Oliveira

The MIT Press eBooks book summary

The Red Queen’s Race

Arlindo L. Oliveira

The MIT Press eBooks book summary

Brains, Minds, and Machines

Arlindo L. Oliveira

The MIT Press eBooks book summary

How the Brain Works

Arlindo L. Oliveira

The MIT Press eBooks book summary

Challenges and Promises

Arlindo L. Oliveira

The MIT Press eBooks book summary

The Digital Mind: How Science Is Redefining Humanity

Arlindo L. Oliveira

book summary

The Digital Mind

Arlindo L. Oliveira

The MIT Press eBooks book summary

2016

LEMPEL-ZIV SLIDING WINDOW UPDATE WITH SUFFIX ARRAYS

Artur Ferreira, Arlindo L. Oliveira, Mário A. T. Figueiredo

Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) conference summary

ELIXIR in a Business Model Canvas

José Borbinha, João Cardoso, Inês Chaves, Bruno Cesar Pereira da Costa, Cymon Cox, Daniel Faria, Pedro Fernandes, Celia María Gonzalo Miguel, Ahmad Nadali, Daniel Sobral, Arlindo L. Oliveira, Mário J. Silva

Open MIND conference summary

The ELIXIR channel in F1000Research

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

F1000Research journal summary

DegreeCox – a network-based regularization method for survival analysis

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

BMC Bioinformatics journal summary

2014

An Adaptive Step-Size Least Mean Square Algorithm for Electric Power Systems Frequency Estimation in protective relays

Gustavo Marchesan, Arlindo L. Oliveira, Ghendy Cardoso, Adriano Peres de Morais, L. Mariotto

conference summary

2013

Using Information Interaction to Discover Epistatic Effects in Complex Diseases

Orlando Anunciação, Susana Vinga, Arlindo L. Oliveira

PLoS ONE journal summary

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 summary

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 summary

Efficient and Accurate Haplotype Inference by Combining Parsimony and Pedigree Information

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

Lecture notes in computer science book

2011

Improved Model Checking Techniques for State Space Analysis of Gene Regulatory Networks

Helio Pais, Kenneth L. McMillan, Ellen Sentovich, Ana T. Freitas, Arlindo L. Oliveira

IGI Global eBooks book summary

Quantitative Modeling the Saccharomyces cerevisiae FLR1 Regulatory Network Using an S-System Formalism

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

conference summary

Using systems biology approaches to study a multidrug resistance network

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

conference summary

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 summary

Sliding Window Update Using Suffix Arrays

Artur Ferreira, Arlindo L. Oliveira, Mário A. T. Figueiredo

conference summary

On Community Detection in Very Large Networks

Alexandre P. Francisco, Arlindo L. Oliveira

Communications in computer and information science book

Mining query log graphs towards a query folksonomy

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

Concurrency and Computation Practice and Experience journal summary

Fully Generalized Graph Cores

Alexandre P. Francisco, Arlindo L. Oliveira

Communications in computer and information science book

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 summary

Dissertations supervised

Text Segmentation by TextTiling with Modern Neural Retrieval Models

Supervised by Bruno Martins, Arlindo L. Oliveira

Open for application MSc

Sign Language Recognition with Large Vision-and-Language Models

Supervised by Bruno Martins, Arlindo L. Oliveira

Open for application MSc

Improving Medical Image Segmentation through Human Feedback and Reward Modeling

Supervised by Arlindo L. Oliveira

Open for application MSc

AI-Driven Pulmonary Function Analysis for Respiratory Screening

Supervised by Arlindo L. Oliveira

Open for application MSc

"Agentification" in a Manufacturing Context

Supervised by Arlindo L. Oliveira

Open for application MSc

Optimization Model for Biomass Plant Control

Supervised by Arlindo L. Oliveira

Open for application MSc

Adaptive Early Vision Networks: Learning Biologically Constrained Front-Ends for Robust Visual Recognition

Supervised by Arlindo L. Oliveira, Tiago Marques

Open for application MSc

Multi-Modal Autoencoder Framework for Predicting Plasma Proteome from Genomic Data Using AlphaGenome

Supervised by Arlindo L. Oliveira, Inês Duarte

Open for application MSc

Enhancing Fine-Grained Perceptual Understanding of Scientific Graphs in Vision Language Models

Supervised by Arlindo L. Oliveira, Hélder Dias

Open for application MSc

Generation of New Scientific Knowledge using LLMs

Supervised by Arlindo L. Oliveira, Vitória Cruz

Open for application MSc

Improving Retrieval Augmented Generation using LLMs

Supervised by Arlindo L. Oliveira

Open for application MSc

Multimodal Document Representation Learning

Supervised by Arlindo L. Oliveira

Open for application MSc

Deep neural network architectures for dual process computation

João Meneses Santos

Supervised by Arlindo L. Oliveira, Bruno Martins

Ongoing MSc

Assessing Large Language Models for information verification in Portuguese

Supervised by Arlindo L. Oliveira, Nuno Cardoso

Ongoing MSc

Handling Portuguese Varieties with Pre-Trained Language Models

Rodrigo Laia

Supervised by Bruno Martins, Arlindo L. Oliveira

Ongoing MSc

Reasoning in Large Language Models and the Dual-Process Theory of Cognition

Adrian Graur

Supervised by Arlindo L. Oliveira

Ongoing MSc

An Intelligent Software Agent for Personalized Tutoring

Natan Gloeh

Supervised by Arlindo L. Oliveira

Ongoing MSc

Developing a Sense of Humour in Large Language Models

Duarte Sousa

Supervised by Arlindo L. Oliveira

Ongoing MSc

Unmixing mass spectra using machine learning for species identification

Vasco Paisana

Supervised by Arlindo L. Oliveira

Ongoing MSc

Predicting Frequency and Claims of Health Insurance with Machine Learning techniques

Pedro Octávio Couto Gonçalves

Supervised by Arlindo L. Oliveira, Luís Miguel Veiga Vaz Caldas de Oliveira.

Finished MSc

WeatherIST - iOS application for detailed weather prevision in Continental Portugal

Tiago João Alves Duarte

Supervised by Arlindo L. Oliveira

Finished MSc

Imputation Techniques for Clinical Data of Ischemic Stroke Patients

Filipa de Matos Marques

Supervised by Arlindo L. Oliveira, Alexandre Paulo Lourenço Francisco.

Finished MSc

Applying Deep Learning to Medical Images

Ricardo Jorge da Silva Diniz

Supervised by Arlindo L. Oliveira, Mário Alexandre Teles de Figueiredo.

Finished MSc

Automated Assessment of Coronary Artery Stenosis in X-ray Angiography using Deep Neural Networks

Dinis Lourenço Tavares Rodrigues

Supervised by Arlindo L. Oliveira, Mário Alexandre Teles de Figueiredo.

Finished MSc

Deep Convolutional Encoder-Decoder Architectures for Clinically Relevant Coronary Artery Segmentation

João Lourenço Coelho da Silva

Supervised by Arlindo L. Oliveira, Mário Alexandre Teles de Figueiredo.

Finished MSc

Pathological Analysis of Tissues using Deep Neural Networks

Xavier Abreu Dias

Supervised by Arlindo L. Oliveira, João Cassis.

Finished MSc

Modelling and Inference of Gene Regulatory Networks

José Miguel Ranhada Vellez Caldas

Supervised by Arlindo L. Oliveira

Finished MSc

Biological Data Processing Using Grid Technologies

Sérgio Mendes Costa

Supervised by Arlindo L. Oliveira

Finished MSc

Automatic Annotation of Unstructured Fields in Medical Databases

Margarida Andreia Rosa Correia

Supervised by Arlindo L. Oliveira, Maria Luísa Torres Ribeiro Marques da Silva Coheur.

Finished MSc

MyWatson: A system for interactive acess of personal records

Pedro Miguel dos Santos Duarte

Supervised by Arlindo L. Oliveira

Finished MSc

Application of Deep Learning Techniques to the Diagnosis of Medical Images

Pedro Miguel Carreto Vaz

Supervised by Arlindo L. Oliveira

Finished MSc

Combining off and on-policy training in Deep Reinforcement

Alexandre João Gomes Borges

Supervised by Arlindo L. Oliveira

Finished MSc

Evaluating generalization in Deep Reinforcement Learning with Procedural Generated Environments

Miguel Borges Freire

Supervised by Arlindo L. Oliveira

Finished MSc

Using Knowledge Graphs to model Digital Footprints

André Carlos Ruano Andrade Cavalheiro

Supervised by Arlindo L. Oliveira

Finished MSc

Improving the Performance of Deep Neural Networks in Vision Tasks with Attention Mechanisms.

Rafael Gamanho Pedro

Supervised by Arlindo L. Oliveira

Finished MSc

A Modular Architecture for Model-Based Deep Reinforcement Learning

Tiago João Gaspar Ribeiro de Oliveira

Supervised by Arlindo L. Oliveira

Finished MSc

Using a Siamese Network to Accurately Detect Ischemic Stroke in Computed Tomography Scans

Supervised by Arlindo L. Oliveira, Catarina Fonseca

Finished MSc

Old photo and image restoration using deep learning techniques

Supervised by Arlindo L. Oliveira

Finished MSc

Neural Models for Generating Clinically Accurate Chest X-Ray Reports

Supervised by Arlindo L. Oliveira, Bruno Martins

Finished MSc

Pretraining the Vision Transformer using self-supervised methods for vision-based deep reinforcement learning

Supervised by Arlindo L. Oliveira

Finished MSc

Transaction-Based Entity Monitoring in a Client Due Diligence Context

Oleksandr Stopchak

Supervised by Arlindo L. Oliveira, Jacopo Bono

Finished MSc

Towards Improving Ischemic Stroke Functional Outcome Prediction with Computed Tomography Brain Scans Using Deep Learning

Gonçalo Oliveira

Supervised by Arlindo L. Oliveira, Catarina Fonseca

Finished MSc

Efficient Algorithms for Medical Image Segmentation

Supervised by Arlindo L. Oliveira

Finished MSc

Deep learning when data is scarce

Ana Pimenta Alves

Supervised by Arlindo Manuel Limede de Oliveira

Finished MSc

Operation log monitoring using machine learning

Supervised by Arlindo L. Oliveira, Fernando Silva

Finished MSc

Stenosis detection in coronary X-ray angiographies

Supervised by Arlindo L. Oliveira, Miguel Menezes

Finished MSc

Using graph embeddings to explore deep neural network architectures

Supervised by Arlindo L. Oliveira

Finished MSc

Using sequences of coronary angiograms to quantify the severity of stenosis

Mariana Serrão

Supervised by Arlindo L. Oliveira

Finished MSc

Using Large Language Models do solve the Abstraction and Reasoning Challenge

Guilherme Costa

Supervised by Arlindo L. Oliveira

Finished MSc

Representation learning of animal behavior

Gonçalo Goulart Oliveira

Supervised by Arlindo L. Oliveira, Adrien Jouary

Finished MSc

Using biological features to improve deep neural network models for vision

Lucas Alergy

Supervised by Arlindo L. Oliveira, Tiago Marques

Finished MSc

Modelos de causalidade para determinação do impacto de acções comerciais

Supervised by Arlindo L. Oliveira, Filipa Marques

Finished MSc

Using large language models to interact with personal information systems

Supervised by Arlindo L. Oliveira

Finished MSc

Biologically inspired CNNs for Medical Imaging tasks

Daniela Carvalho

Supervised by Arlindo L. Oliveira, Tiago Marques

Finished MSc

Stroke Segmentation from Computed Tomography scans

Supervised by Arlindo L. Oliveira

Finished MSc

Transfer single-cell foundation models to predict drug resistance in cancer

Gonçalo Gonçalves

Supervised by Arlindo L. Oliveira, Emanuel Gonçalves

Finished MSc

Hybrid Prompt Optimization for Sparse Autoencoder Feature Visualization in Large Language Models

João Marques Cardoso

Supervised by Arlindo L. Oliveira, Bruno Martins

Finished MSc

Siamese Transformer Networks for Improving Address Matching

Supervised by Arlindo L. Oliveira

Finished MSc