Antonio Benítez-Hidalgo

We present a Kubernetes-based, open source MLOps framework to streamline the lifecycle management of machine learning models in production environments. We compared state-of-the-art MLOps tools and frameworks, demonstrating that ours meets the same features as proprietary options, such as Amazon SageMaker.

Reasoning is the process of inferring new knowledge and identifying inconsistencies within ontologies. Traditional techniques often prove inadequate when reasoning over large Knowledge Bases containing millions or billions of facts. This article introduces NORA, a persistent and scalable OWL reasoner built on top of Apache Spark, designed to address the challenges of reasoning over extensive and complex ontologies. NORA exploits the scalability of NoSQL databases to effectively apply inference rules to Big Data ontologies with large ABoxes. To facilitate scalable reasoning, OWL data, including class and property hierarchies and instances, are materialized in the Apache Cassandra database. Spark programs are then evaluated iteratively, uncovering new implicit knowledge from the dataset and leading to enhanced performance and more efficient reasoning over large‐scale ontologies. NORA has undergone a thorough evaluation with different benchmarking ontologies of varying sizes to assess the scalability of the developed solution.

Background: Information provided by high-throughput sequencing platforms allows the collection of content-rich data about biological sequences and their context. Sequence alignment is a bioinformatics approach to identifying regions of similarity in DNA, RNA, or protein sequences. However, there is no consensus about the specific common terminology and representation for sequence alignments. Thus, automatically linking the wide existing knowledge about the sequences with the alignments is challenging. Results: The Sequence Alignment Ontology (SALON) defines a helpful vocabulary for representing and semantically annotating pairwise and multiple sequence alignments. SALON is an OWL 2 ontology that supports automated reasoning for alignments validation and retrieving complementary information from public databases under the Open Linked Data approach. This will reduce the effort needed by scientists to interpret the sequence alignment results. Conclusions: SALON defines a full range of controlled terminology in the domain of sequence alignments. It can be used as a mediated schema to integrate data from different sources and validate acquired knowledge.

Multiple sequence alignment (MSA) consists of finding the optimal alignment of three or more biological sequences to identify highly conserved regions that may be the result of similarities and relationships between the sequences. MSA is an optimization problem with NP-hard complexity (non-deterministic polynomial-time hardness), because the time needed to find optimal alignments raises exponentially along with the number of sequences and their length. Furthermore, the problem becomes multiobjective when more than one score is considered to assess the quality of an alignment, such as maximizing the percentage of totally conserved columns and minimizing the number of gaps. Our motivation is to provide a Python tool for solving MSA problems using evolutionary algorithms, a nonexact stochastic optimization approach that has proven to be effective to solve multiobjective problems. The software tool we have developed, called Sequoya, is written in the Python programming language, which offers a broad set of libraries for data analysis, visualization and parallelism. Thus, Sequoya offers a graphical tool to visualize the progress of the optimization in real time, the ability to guide the search toward a preferred region in run-time, parallel support to distribute the computation among nodes in a distributed computing system, and a graphical component to assist in the analysis of the solutions found at the end of the optimization. Sequoya can be freely obtained from the Python Package Index (pip) or, alternatively, it can be downloaded from Github at https://github.com/benhid/Sequoya. Supplementary data are available at Bioinformatics online.

This paper describes jMetalPy, an object-oriented Python-based framework for multi-objective optimization with metaheuristic techniques. Building upon our experiences with the well-known jMetal framework, we have developed a new multi-objective optimization software platform aiming not only at replicating the former one in a different programming language, but also at taking advantage of the full feature set of Python, including its facilities for fast prototyping and the large amount of available libraries for data processing, data analysis, data visualization, and high-performance computing. As a result, jMetalPy provides an environment for solving multi-objective optimization problems focused not only on traditional metaheuristics, but also on techniques supporting preference articulation and dynamic problems, along with a rich set of features related to the automatic generation of statistical data from the results generated, as well as the real-time and interactive visualization of the Pareto front approximations produced by the algorithms. jMetalPy offers additionally support for parallel computing in multicore and cluster systems. We include some use cases to explore the main features of jMetalPy and to illustrate how to work with it.