Andreia Sofia Teixeira

Andreia Sofia Teixeira
University of Lisbon | UL · Faculty of Science

PhD. andreiasofiateixeira.com

About

40
Publications
7,573
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101
Citations
Introduction
Complex Networks (preferably from an edge perspective). Computational Biology/Epidemiology. Network Neuroscience. Cognitive Network Science. Game Theory (both with Social and Individual Learning). Structural Balance.

Publications

Publications (40)
Article
Full-text available
Trees, including minimum spanning trees (MSTs), are commonly used in phylogenetic studies. But, for the research community, it may be unclear that the presented tree is just a hypothesis, chosen from among many possible alternatives. In this scenario, it is important to quantify our confidence in both the trees and the branches/edges included in su...
Conference Paper
Full-text available
We present a new edge betweenness metric for undirected and weighted graphs. This metric is defined as the fraction of minimum spanning trees where a given edge is present and it was motivated by the necessity of evaluating phylogenetic trees. Moreover we provide results and methods concerning the exact computation of this metric based on the well...
Article
Full-text available
Functional connectivity (FC) describes the statistical dependence between neuronal populations or brain regions in resting-state fMRI studies and is commonly estimated as the Pearson correlation of time courses. Clustering or community detection reveals densely coupled sets of regions constituting resting-state networks or functional systems. These...
Article
Full-text available
Understanding how people who commit suicide perceive their cognitive states and emotions represents an important open scientific challenge. We build upon cognitive network science, psycholinguistics and semantic frame theory to introduce a network representation of suicidal ideation as expressed in multiple suicide notes. By reconstructing the know...
Article
Full-text available
From social contracts to climate agreements, individuals engage in groups that must collectively reach decisions with varying levels of equality and fairness. These dilemmas also pervade distributed artificial intelligence, in domains such as automated negotiation, conflict resolution, or resource allocation, which aim to engineer self-organized gr...
Article
Full-text available
Epidemic control often requires optimal distribution of available vaccines and prophylactic tools, to protect from infection those susceptible. Well-established theory recommends prioritizing those at the highest risk of exposure. But the risk is hard to estimate, especially for diseases involving stigma and marginalization. We address this conundr...
Conference Paper
Full-text available
When we address phylogeny, telecommunication/electric networks, among other networks, we are often interested in studying measures that go beyond shortest path/fixed distance properties-if we want to know how strongly connected a network is, i.e., which links are fundamental to keep the network connected and which are redundant. In algorithms for p...
Chapter
Transcriptional regulatory networks are responsible for controlling gene expression. These networks are composed of many interactions between transcription factors and their target genes. Carrying a combinatorial nature that encompasses several regulatory processes, they allow an organism to respond to disturbances that may occur in the surrounding...
Preprint
Full-text available
Suicide remains a serious public-health concern that is difficult to accurately predict in real-world settings. To identify potential predictors of suicide, we examined the emotional content of suicide notes using methods from cognitive network science. Specifically, we compared the co-occurrence networks of suicide notes with those constructed out...
Preprint
Communicating one's mindset means transmitting complex relationships between concepts and emotions. Using cognitive network science, we reconstruct the mindset around suicide as communicated in 139 genuine suicide notes. Despite their negative context, suicide notes are surprisingly positively valenced and their ending statements are markedly more...
Preprint
Full-text available
Phenotypic Disease Networks (PDNs), which capture comorbidities, can be used to study phenotypic differences between demographics. Networks are an useful way to understand disease progression as they tend to occur in the vicinity of current conditions. Additionally, the local and global structure of these networks, in combination with centrality me...
Poster
Full-text available
From employment contracts to climate agreements, individuals often engage in groups that must reach decisions with varying levels of fairness. These dilemmas also pervade AI, e.g. in automated negotiation, conflict resolution or resource allocation. As evidenced by the Ultimatum Game, payoff maximization is frequently at odds with fairness. Eliciti...
Conference Paper
Full-text available
From employment contracts to climate agreements, individuals often engage in groups that must reach decisions with varying levels of fairness. These dilemmas also pervade AI, e.g. in automated negotiation , conflict resolution or resource allocation. As evidenced by the Ultimatum Game, payoff maximization is frequently at odds with fairness. Elicit...
Preprint
Full-text available
From social contracts to climate agreements, individuals engage in groups that must collectively reach decisions with varying levels of equality and fairness. These dilemmas also pervade Distributed Artificial Intelligence, in domains such as automated negotiation, conflict resolution or resource allocation. As evidenced by the well-known Ultimatum...
Book
This book contains contributions presented at the 12th International Conference on Complex Networks (CompleNet), 24-26 May 2021. CompleNet is an international conference on complex networks that brings together researchers and practitioners from diverse disciplines—from sociology, biology, physics, and computer science—who share a passion to better...
Article
Full-text available
Resources such as FrameNet, which provide sets of semantic frame definitions and annotated textual data that maps into the evoked frames, are important for several NLP tasks. However, they are expensive to build and, consequently, are unavailable for many languages and domains. Thus, approaches able to induce semantic frames in an unsupervised mann...
Preprint
Full-text available
Functional connectivity (FC) describes the statistical dependence between brain regions in resting-state fMRI studies and is usually estimated as the Pearson correlation of time courses. Clustering reveals densely coupled sets of regions constituting a set of resting-state networks or functional systems. These systems manifest most clearly when FC...
Preprint
Full-text available
Understanding how people who commit suicide perceive their cognitive states and emotions represents a crucially open scientific challenge. We build upon cognitive network science, psycholinguistics and semantic frame theory to introduce a network representation of suicidal ideation as expressed in multiple suicide notes. By reconstructing the knowl...
Conference Paper
Full-text available
Resources such as FrameNet provide semantic information that is important for multiple tasks. However, they are expensive to build and, consequently, are unavailable for many languages and domains. Thus, approaches able to induce semantic frames in an unsupervised manner are highly valuable. In this paper we approach that task from a network perspe...
Thesis
Full-text available
If we carefully observe our daily lives and the systems in which we participate, we naturally perceive that everything is somehow connected. From species evolution to social relations, acknowledging all the supply chain systems we depend on, networks portray the simplest representation of these systems. Notwithstanding this simplicity, these networ...
Poster
Full-text available
Social media often reveals a complex interplay between positive and negative ties. And real online social networks are proven to show high social balance. Yet, the origin of such complex patterns of interaction remains largely elusive. In this work we study how third parties may sway our perception of others. We build a model of peer-influence rely...
Preprint
Full-text available
Sexual contacts are the main spreading route of HIV. This puts sex workers at higher risk of infection even in populations where HIV prevalence is moderate or low. Alongside condom use, Pre-Exposure Prophylaxis (PrEP) is an effective tool for sex workers to reduce their risk of HIV acquisition. However, PrEP provides no direct protection against ST...
Chapter
Full-text available
Measuring the inner characteristics of financial markets risks have been proven to be key at understanding what promotes financial instability and volatility swings. Advances in complex network analysis have shown the capability to characterize the specificities of financial networks, ranging from credit networks, volatility networks, and supply-ch...
Article
Full-text available
RNA-Seq is a Next-Generation Sequencing (NGS) protocol for sequencing the messenger RNA in a cell and generates millions of short sequence fragments, reads, in a single run. These reads can be used to measure levels of gene expression and to identify novel splice variants of genes. One of the critical steps in an RNA-Seq experiment is mapping NGS r...
Article
The understanding of bacterial population genetics and evolution is crucial in epidemic outbreak studies and pathogen surveillance. However, all epidemiological studies are limited to their sampling capacities which, by being usually biased or limited due to economic constraints, can hamper the real knowledge of the bacterial population structure o...
Article
Full-text available
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle graphs we prove that this approach significantly outperforms existing algorithms. For general graphs we obtain...
Conference Paper
Full-text available
Large-scale population genetics studies are fundamental for phylogenetic and epidemiology analysis of pathogens. And the validation of both evolutionary models and methods used in such studies depend on large data analysis. It is, however, unrealistic to work with large datasets as only rather small samples of the real pathogen population are avail...
Presentation
Full-text available
Social media often reveals a complex interplay between positive and negative ties. Yet, the origin of such complex patterns of interaction remains largely elusive. In this paper we study how third parties may sway our perception of others. Our model relies on the analysis of all triadic relations taking into account the influence and relations with...
Conference Paper
Full-text available
Social media often reveals a complex interplay between positive and negative ties. Yet, the origin of such complex patterns of interaction remains largely elusive. In this paper we study how third parties may sway our perception of others. Our model relies on the analysis of all triadic relations taking into account the influence and relations with...
Presentation
Full-text available
BACKGROUND: The RNA-Seq protocol for sequencing the messenger RNA in a cell generates millions of short sequence fragments in a single run. These fragments, or reads, can be used to measure levels of gene expression and to identify novel splice variants of genes. One of the critical steps in an RNA-Seq experiment is mapping NGS reads to the referen...
Presentation
Full-text available
Presentation about Spanning Edge Betweenness explaining the theory and the applications.
Poster
Full-text available
In this work we address the simulation of genetic evolution of bacterial populations in presence of host contact networks. In particular we consider traditional evolution models combined with well mixed and not well mixed host populations, the latter being more realistic. To our knowledge this is the first approach to consider not well mixed host po...
Poster
Full-text available
We present a study about spanning edge betweenness, an edge-based metric for complex network analysis that is defined as the probability of an edge being part of a minimum spanning tree. This probability reflects how redundant an edge is in what concerns the connectivity of a given network and, hence, its value gives information about the network top...
Chapter
Full-text available
In this paper we present a study about spanning edge betweenness, an edge-based metric for complex network analysis that is defined as the probability of an edge being part of a minimum spanning tree . This probability reflects how redundant an edge is in what concerns the connectivity of a given network and, hence, its value gives information abou...
Presentation
Full-text available
In the era of Big Data, parallelization have become crucial for efficient and timely large-scale analysis. In particular, MapReduce programming model has gain a new enthusiasm with the forthcoming of frameworks as Apache Hadoop or Apache Spark, turning embarrassingly parallel problems and graph algorithms easier and faster to solve with these new fra...

Network

Cited By

Projects

Projects (7)
Project
We are interested in studying emergence of fairness and cooperation using properties of complex networks.
Project
Using Network Neuroscience tools and as well as other graph theory and cognitive science theories, we aim to reveal fundamental properties and dynamics of both structural and functional connectivity of brain networks.
Project
Efficient algorithms and data structures for DNA/RNA alignment. HPC approach coming.