Leonardo Guerreiro Azevedo

Emilio Vital Brazil, Eduardo Soares, Lucas Villa Real et al.

Data is a critical element in any discovery process. In the last decades, we observed exponential growth in the volume of available data and the technology to manipulate it. However, data is only practical when one can structure it for a well-defined task. For instance, we need a corpus of text broken into sentences to train a natural language machine-learning model. In this work, we will use the token \textit{dataset} to designate a structured set of data built to perform a well-defined task. Moreover, the dataset will be used in most cases as a blueprint of an entity that at any moment can be stored as a table. Specifically, in science, each area has unique forms to organize, gather and handle its datasets. We believe that datasets must be a first-class entity in any knowledge-intensive process, and all workflows should have exceptional attention to datasets' lifecycle, from their gathering to uses and evolution. We advocate that science and engineering discovery processes are extreme instances of the need for such organization on datasets, claiming for new approaches and tooling. Furthermore, these requirements are more evident when the discovery workflow uses artificial intelligence methods to empower the subject-matter expert. In this work, we discuss an approach to bringing datasets as a critical entity in the discovery process in science. We illustrate some concepts using material discovery as a use case. We chose this domain because it leverages many significant problems that can be generalized to other science fields.

Guilherme Lima, João M. B. Rodrigues, Marcelo Machado et al.

We present a Wikidata-based framework, called KIF, for virtually integrating heterogeneous knowledge sources. KIF is written in Python and is released as open-source. It leverages Wikidata's data model and vocabulary plus user-defined mappings to construct a unified view of the underlying sources while keeping track of the context and provenance of their statements. The underlying sources can be triplestores, relational databases, CSV files, etc., which may or may not use the vocabulary and RDF encoding of Wikidata. The end result is a virtual knowledge base which behaves like an "extended Wikidata" and which can be queried using a simple but expressive pattern language, defined in terms of Wikidata's data model. In this paper, we present the design and implementation of KIF, discuss how we have used it to solve a real integration problem in the domain of chemistry (involving Wikidata, PubChem, and IBM CIRCA), and present experimental results on the performance and overhead of KIF

Roberto Miele, Leonardo Azevedo

Probabilistic seismic inverse modeling often requires the prediction of both spatially correlated geological heterogeneities (e.g., facies) and continuous parameters (e.g., rock and elastic properties). Generative adversarial networks (GANs) provide an efficient training-image-based simulation framework capable of reproducing complex geological models with high accuracy and comparably low generative cost. However, their application in stochastic geophysical inversion for multivariate property prediction is limited, as representing multiple coupled properties requires large and unstable networks with high memory and training demands. A more recent variant of GANs with spatially adaptive denormalization (SPADE-GAN) enables the direct conditioning of facies spatial distributions on local probability maps. Leveraging on such features, an iterative geostatistical inversion algorithm is proposed, SPADE-GANInv, integrating a pre-trained SPADE-GAN with geostatistical simulation, for the prediction of facies and multiple correlated continuous properties from seismic data. The SPADE-GAN is trained to reproduce realistic facies geometries, while sequential stochastic co-simulation predicts the spatial variability of the facies-dependent continuous properties. At each iteration, a set of subsurface realizations is generated and used to compute synthetic seismic data. The realizations providing the highest similarity coefficient to the observed data are used to update the subsurface probability models in the next iteration. The method is demonstrated on both 2-D synthetic scenarios and field data, targeting the prediction of facies, porosity, and acoustic impedance from full-stack seismic data. Results show that the algorithm enables accurate multivariate prediction, mitigates the impact of biased prior data, and accommodates additional local conditioning such as well logs.

Maximillien de Bayser, Vinicius Segura, Leonardo Guerreiro Azevedo et al.

There is a gap in scientific information systems development concerning modern software engineering and scientific computing. Historically, software engineering methodologies have been perceived as an unwanted accidental complexity to computational scientists in their scientific systems development. More recent trends, like the end of Moore's law and the subsequent diversification of hardware platforms, combined with the increasing multidisciplinarity of science itself have exacerbated the problem because self-taught "end user developers" are not familiar with the disciplines needed to tackle this increased complexity. On a more positive note, agile programming methods have approached software development practices to the way scientific software is produced. In this work, we present the experience of a multi-year industry research project where agile methods, microservices and DevOps were applied. Our goal is to validate the hypothesis that the use of microservices would allow computational scientists to work in the more minimalistic prototype-oriented way that they prefer while the software engineering team would handle the integration. Hence, scientific multidisciplinary systems would gain in a twofold way: (i) Subject Matter Experts(SME) use their preferable tools to develop the specific scientific part of the system; (ii) software engineers provide the high quality software code for the system delivery.

Mauro Lourenço Pedra, Mônica Ferreira da Silva, Leonardo Guerreiro Azevedo

DevOps is an approach based on lean and agile principles in which business, development, operations, and quality teams cooperate to deliver software continuously aiming at reducing time to market, and receiving constant feedback from customers. However, implementing DevOps can be a complex and challenging mission due it requires significant paradigm shift. Consequently, many failures and misconceptions can occur about DevOps adoption by organizations, despite its numerous benefits. This work identifies, describes, and compares different perspectives related to DevOps adoption in academy and industry. The perspectives can be understood as factors or variables that influence or help to understand the DevOps journey. We employed a sequential multi-method research approach, including Systematic Literature Review (SLR) and Case Study. As a result, eight perspectives were found: concepts, models, principles, practices, difficulties, challenges, benefits, and strategies. More specifically, the SLR produced 390 items, which can be understood as occurrences of a perspective. The conducted case study confirmed 75 items, corroborating the SLR findings, while another 29 items emerged. This global view on DevOps adoption may guide beginners, both theorists, and practitioners, to make the necessary organizational transformation less painful.

Mário Cardoso, André Cavalheiro, Alexandre Borges et al.

Europe was hit hard by the COVID-19 pandemic and Portugal was one of the most affected countries, having suffered three waves in the first twelve months. Approximately between Jan 19th and Feb 5th 2021 Portugal was the country in the world with the largest incidence rate, with 14-days incidence rates per 100,000 inhabitants in excess of 1000. Despite its importance, accurate prediction of the geospatial evolution of COVID-19 remains a challenge, since existing analytical methods fail to capture the complex dynamics that result from both the contagion within a region and the spreading of the infection from infected neighboring regions. We use a previously developed methodology and official municipality level data from the Portuguese Directorate-General for Health (DGS), relative to the first twelve months of the pandemic, to compute an estimate of the incidence rate in each location of mainland Portugal. The resulting sequence of incidence rate maps was then used as a gold standard to test the effectiveness of different approaches in the prediction of the spatial-temporal evolution of the incidence rate. Four different methods were tested: a simple cell level autoregressive moving average (ARMA) model, a cell level vector autoregressive (VAR) model, a municipality-by-municipality compartmental SIRD model followed by direct block sequential simulation and a convolutional sequence-to-sequence neural network model based on the STConvS2S architecture. We conclude that the convolutional sequence-to-sequence neural network is the best performing method, when predicting the medium-term future incidence rate, using the available information.

Renan Souza, Leonardo G. Azevedo, Vítor Lourenço et al.

Machine Learning (ML) has already fundamentally changed several businesses. More recently, it has also been profoundly impacting the computational science and engineering domains, like geoscience, climate science, and health science. In these domains, users need to perform comprehensive data analyses combining scientific data and ML models to provide for critical requirements, such as reproducibility, model explainability, and experiment data understanding. However, scientific ML is multidisciplinary, heterogeneous, and affected by the physical constraints of the domain, making such analyses even more challenging. In this work, we leverage workflow provenance techniques to build a holistic view to support the lifecycle of scientific ML. We contribute with (i) characterization of the lifecycle and taxonomy for data analyses; (ii) design principles to build this view, with a W3C PROV compliant data representation and a reference system architecture; and (iii) lessons learned after an evaluation in an Oil & Gas case using an HPC cluster with 393 nodes and 946 GPUs. The experiments show that the principles enable queries that integrate domain semantics with ML models while keeping low overhead (<1%), high scalability, and an order of magnitude of query acceleration under certain workloads against without our representation.

Renan Souza, Leonardo Azevedo, Vítor Lourenço et al.

Machine Learning (ML) has become essential in several industries. In Computational Science and Engineering (CSE), the complexity of the ML lifecycle comes from the large variety of data, scientists' expertise, tools, and workflows. If data are not tracked properly during the lifecycle, it becomes unfeasible to recreate a ML model from scratch or to explain to stakeholders how it was created. The main limitation of provenance tracking solutions is that they cannot cope with provenance capture and integration of domain and ML data processed in the multiple workflows in the lifecycle while keeping the provenance capture overhead low. To handle this problem, in this paper we contribute with a detailed characterization of provenance data in the ML lifecycle in CSE; a new provenance data representation, called PROV-ML, built on top of W3C PROV and ML Schema; and extensions to a system that tracks provenance from multiple workflows to address the characteristics of ML and CSE, and to allow for provenance queries with a standard vocabulary. We show a practical use in a real case in the Oil and Gas industry, along with its evaluation using 48 GPUs in parallel.