arXiv subjects

Fabio Lopes

Publications and source records attributed to Fabio Lopes.

10 recordsLinked to original sources

arXiv2025

Accelerating discovery across scientific disciplines through reproducible workflows with AiiDAlab

With ever-increasing computational capabilities, robust and automated research workflows have become essential for orchestrating large numbers of interdependent simulations. However, significant technical expertise is still required to configure execution environments, define calculation inputs, interpret outputs, and manage the complexity of parallel code execution on remote machines. To address these challenges, we developed AiiDAlab, a Jupyter-based web platform powered by the AiiDA computational infrastructure that provides a framework for managing and automating computational workflows while ensuring reproducibility through full provenance tracking. Through a collection of open-source user-friendly applications, AiiDAlab enables scientists to set up, execute, and analyze complex computational workflows without interacting directly with the underlying technical details, allowing them to focus on their research questions. In this paper, we discuss how AiiDAlab has matured over the past few years, expanding beyond computational materials science and its AiiDA origins. We present recent developments towards integrating with electronic laboratory notebooks (ELNs) for FAIR-compliant data management, adoption in large-scale facilities for secure access to experimental data and analytical tools, and applications in educational settings. Together with community-driven efforts to simplify onboarding, improve access to computational resources, and support large-scale data workflows, these advancements position AiiDAlab as a powerful platform for accelerating scientific discovery and fostering collaboration across disciplines.

cs.DC↗

arXiv2024

A stochastic model for immune response with mutations and evolution: the non-spatial setting

We consider a stochastic model for a pathogen population in the presence of an immune response, in which pathogen types are partially ordered by ancestry and the immune system must eliminate ancestor types before it can eliminate their descendants. In this model, pathogens reproduce independently at rate $\lambda>0$ and, at each birth, a mutation occurs with probability $r\in(0,1]$, producing a novel type that is antigenically distinct and whose elimination by the immune system is delayed relative to its ancestors. We provide an explicit characterization of the survival--extinction phase transition and compute the expected total progeny in the subcritical regime. We then extend the model by allowing mutations to be deleterious: conditional on mutation, with probability $p\in(0,1]$ the mutation is beneficial and with probability $1-p$ it is deleterious, producing a sterile offspring. For this extension, we obtain an explicit survival criterion in terms of $(\lambda,r,p)$ and identify parameter regimes in which survival is possible only for an intermediate range of mutation probabilities, reflecting the balance between immune escape and mutational load.

math.PR↗

arXiv2022

Imaging the time series of one single referenced EEG electrode for Epileptic Seizures Risk Analysis

The time series captured by a single scalp electrode (plus the reference electrode) of refractory epileptic patients is used to forecast seizures susceptibility. The time series is preprocessed, segmented, and each segment transformed into an image, using three different known methods: Recurrence Plot, Gramian Angular Field, Markov Transition Field. The likelihood of the occurrence of a seizure in a future predefined time window is computed by averaging the output of the softmax layer of a CNN, differently from the usual consideration of the output of the classification layer. By thresholding this likelihood, seizure forecasting has better performance. Interestingly, for almost every patient, the best threshold was different from 50%. The results show that this technique can predict with good results for some seizures and patients. However, more tests, namely more patients and more seizures, are needed to better understand the real potential of this technique.

cs.LG↗

arXiv2022

Epileptic Seizure Risk Assessment by Multi-Channel Imaging of the EEG

Refractory epileptic patients can suffer a seizure at any moment. Seizure prediction would substantially improve their lives. In this work, based on scalp EEG and its transformation into images, the likelihood of an epileptic seizure occurring at any moment is computed using an average of the softmax layer output (the likelihood) of a CNN, instead of the output of the classification layer. Results show that by analyzing the likelihood and thresholding it, prediction has higher sensitivity or a lower FPR/h. The best threshold for the likelihood was higher than 50% for 5 patients, and was lower for the remaining 36. However, more testing is needed, especially in new seizures, to better assess the real performance of this method. This work is a proof of concept with a positive outlook.

eess.SP↗

arXiv2019

Competing frogs on $\mathbb{Z}^d$

A two-type version of the frog model on $\mathbb{Z}^d$ is formulated, where active type $i$ particles move according to lazy random walks with probability $p_i$ of jumping in each time step ($i=1,2$). Each site is independently assigned a random number of particles. At time 0, the particles at the origin are activated and assigned type 1 and the particles at one other site are activated and assigned type 2, while all other particles are sleeping. When an active type $i$ particle moves to a new site, any sleeping particles there are activated and assigned type $i$, with an arbitrary tie-breaker deciding the type if the site is hit by particles of both types in the same time step. We show that the event $G_i$ that type $i$ activates infinitely many particles has positive probability for all $p_1,p_2\in(0,1]$ ($i=1,2$). Furthermore, if $p_1=p_2$, then the types can coexist in the sense that $\mathbb{P}(G_1\cap G_2)>0$. We also formulate several open problems. For instance, we conjecture that, when the initial number of particles per site has a heavy tail, the types can coexist also when $p_1\neq p_2$.

math.PR↗

arXiv2018

Extinction time for the weaker of two competing SIS epidemics

We consider a simple stochastic model for the spread of a disease caused by two virus strains in a closed homogeneously mixing population of size N. The spread of each strain in the absence of the other one is described by the stochastic logistic SIS epidemic process, and we assume that there is perfect cross-immunity between the two strains, that is, individuals infected by one are temporarily immune to re-infections and infections by the other. For the case where one strain has a strictly larger basic reproductive ratio than the other, and the stronger strain on its own is supercritical (that is, its basic reproductive ratio is larger than 1), we derive precise asymptotic results for the distribution of the time when the weaker strain disappears from the population, that is, its extinction time. We further extend our results to certain parameter values where the difference between the two reproductive ratios may tend to 0 as $N \to \infty$. In proving our results, we illustrate a new approach to a fluid limit approximation for a sequence of Markov chains in the vicinity of a stable fixed point of the limit.

math.PR↗

arXiv2017

Evolution with mass extinction on $\mathbb{T}_d^+$

We propose a stochastic model for evolution through mutation and natural selection of a population that evolves on a $\bbT_d^+$ tree. We think of this model as a way of describing the evolution fitness landscape of a population. We obtain sharp and distinct conditions on the set of parameters for extinction and survival.

math.PR↗

arXiv2017

A spatial epidemic model with site contamination

We introduce the effect of site contamination in a model for spatial epidemic spread and show that the presence of site contamination may have a strict effect on the model in the sense that it can make an otherwise subcritical process supercritical. Each site on $\mathbb{Z}^d$ is independently assigned a random number of particles and these then perform random walks restricted to bounded regions around their home locations. At time 0, the origin is infected along with all its particles. The infection then spread in that an infected particle that jumps to a new site causes the site along with all particles located there to be infected. Also, a healthy particle that jumps to a site where infection is presents, either in that the site is infected or in the presence of infected particles, becomes infected. Particles and sites recover at rate $\lambda$ and $\gamma$, respectively, and then become susceptible to the infection again. We show that, for each given value of $\lambda$, there is a positive probability that the infection survives indefinitely if $\gamma$ is sufficiently small, and that, for each given value of $\gamma$, the infection dies out almost surely if $\lambda$ is large enough. Several open problems and modifications of the model are discussed, and some natural conjectures are supported by simulations.

math.PR↗

arXiv2012

Invariant bipartite random graphs on $\mathbb{R}^d$

Suppose that red and blue points occur in $\mathbb{R}^d$ according to two simple point process with finite intensities $λ_{\mathcal{R}}$ and $λ_{\mathcal{B}}$, respectively. Furthermore, let $ν$ and $μ$ be two probability distributions on the strictly positive integers. Assign independently a random number of stubs (half-edges) to each red and blue point with laws $ν$ and $μ$, respectively. We are interested in translation-invariant schemes to match stubs between points of different colors in order to obtain random bipartite graphs in which each point has a prescribed degree distribution with law $ν$ or $μ$ depending on its color. Let $X$ and $Y$ be random variables with law $ν$ and $μ$, respectively. For a large class of point processes we show that we can obtain such translation-invariant schemes matching a.s. all stubs if and only if \[ λ_{\mathcal{R}} \mathbb{E}(X)= λ_{\mathcal{B}} \mathbb{E}(Y), \] allowing $\infty$ in both sides, when both laws have infinite mean. Furthermore, we study a particular scheme based on the Gale-Shapley stable marriage. For this scheme we give sufficient conditions on $X$ and $Y$ for the presence and absence of infinite components. These results are two-color versions of those obtained by Deijfen, Häggström and Holroyd.

math.PR↗

arXiv2012

Bipartite stable Poisson graphs on R

Let red and blue points be distributed on $\mathbb{R}$ according to two independent Poisson processes $\mathcal{R}$ and $\mathcal{B}$ and let each red (blue) point independently be equipped with a random number of half-edges according to a probability distribution $ν$ ($μ$). We consider translation-invariant bipartite random graphs with vertex classes defined by the point sets of $\mathcal{R}$ and $\mathcal{B}$, respectively, generated by a scheme based on the Gale-Shapley stable marriage for perfectly matching the half-edges. Our main result is that, when all vertices have degree 2 almost surely, then the resulting graph does not contain an infinite component. The two-color model is hence qualitatively different from the one-color model, where Deijfen, Holroyd and Peres have given strong evidence that there is an infinite component. We also present simulation results for other degree distributions.

math.PR↗