Alexandre P. Francisco

Alexandre Francisco, Umberto Biccari, Enrique Zuazua

Inverse design of transport equations can be addressed by using a gradient-adjoint methodology. In this methodology numerical schemes used for the adjoint resolution determine the direction of descent in its iterative algorithm, and consequently the CPU time consumed by the inverse design. As the CPU time constitutes a known bottleneck, it is important to employ light and quick schemes to the adjoint problem. In this regard, we proposed to use the Modified Method of Characteristics (MMOC). Despite not preserving identity conservation, the MMOC is computationally competitive. In this work we investigated the advantage of using the MMOC in comparison with the Lax-Friedrichs and Lax-Wendro? schemes for the inverse design problem. By testing the Doswell frontogenesis equation, we observed that the MMOC can provide more efficient and accurate computation under some simulation conditions.

Miguel E. Coimbra, Lucie Svitáková, Domagoj Vrgoč et al.

Graph databases have become essential tools for managing complex and interconnected data, which is common in areas like social networks, bioinformatics, and recommendation systems. Unlike traditional relational databases, graph databases offer a more natural way to model and query intricate relationships, making them particularly effective for applications that demand flexibility and efficiency in handling interconnected data. Despite their increasing use, graph databases face notable challenges. One significant issue is the irregular nature of graph data, often marked by structural sparsity, such as in its adjacency matrix representation, which can lead to inefficiencies in data read and write operations. Other obstacles include the high computational demands of traversal-based queries, especially within large-scale networks, and complexities in managing transactions in distributed graph environments. Additionally, the reliance on traditional centralized architectures limits the scalability of Online Transaction Processing (OLTP), creating bottlenecks due to contention, CPU overhead, and network bandwidth constraints. This paper presents a thorough survey of graph databases. It begins by examining property models, query languages, and storage architectures, outlining the foundational aspects that users and developers typically engage with. Following this, it provides a detailed analysis of recent advancements in graph database technologies, evaluating these in the context of key aspects such as architecture, deployment, usage, and development, which collectively define the capabilities of graph database solutions.

Luís M. S. Russo, Tobias Dietz, José Rui Figueira et al.

Parity check matrices (PCMs) are used to define linear error correcting codes and ensure reliable information transmission over noisy channels. The set of codewords of such a code is the null space of this binary matrix. We consider the problem of minimizing the number of one-entries in parity-check matrices. In the maximum-likelihood (ML) decoding method, the number of ones in PCMs is directly related to the time required to decode messages. We propose a simple matrix row manipulation heuristic which alters the PCM, but not the code itself. We apply simulated annealing and greedy local searches to obtain PCMs with a small number of one entries quickly, i.e. in a couple of minutes or hours when using mainstream hardware. The resulting matrices provide faster ML decoding procedures, especially for large codes.

Bruno Dantas, Calmenelias Fleitas, Alexandre P. Francisco et al.

Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the following is true for many areas of science: published results are usually hard to reproduce either because data is not available or tools are not readily available, which delays the adoption of new methodologies and hinders innovation. Our focus is on tool readiness and pipelines availability. Even though most tools are freely available, pipelines for data analysis are in general barely described and their configuration is far from trivial, with many parameters to be tuned. In this paper we discuss how to effectively build and use pipelines, relying on state of the art computing technologies to execute them without users need to configure, install and manage tools, servers and complex workflow management systems. We perform an in depth comparative analysis of state of the art frameworks and systems. The NGSPipes framework is proposed showing that we can have public pipelines ready to process and analyse experimental data, produced for instance by high-throughput technologies, but without relying on centralized servers or Web services. The NGSPipes framework and underlying architecture provides a major step towards open science and true collaboration in what concerns tools and pipelines among computational biology researchers and practitioners. We show that it is possible to execute data analysis pipelines in a decentralized and platform independent way. Approaches like the one proposed are crucial for archiving and reusing data analysis pipelines at medium/long-term. NGSPipes framework is freely available at http://ngspipes.github.io/.

Luís M. S. Russo, Alexandre P. Francisco

We present a new algorithm to calculate exact hypervolumes. Given a set of $d$-dimensional points, it computes the hypervolume of the dominated space. Determining this value is an important subroutine of Multiobjective Evolutionary Algorithms (MOEAs). We analyze the "Quick Hypervolume" (QHV) algorithm theoretically and experimentally. The theoretical results are a significant contribution to the current state of the art. Moreover the experimental performance is also very competitive, compared with existing exact hypervolume algorithms. A full description of the algorithm is currently submitted to IEEE Transactions on Evolutionary Computation.