Iván Hidalgo-Cenalmor

Bruno M. Saraiva, Iván Hidalgo-Cenalmor, António D. Brito et al.

Researchers face a persistent barrier when applying computational algorithms with parameter configuration typically demanding programming skills, interfaces differing across environments, and settings rarely persisting between sessions. This fragmentation forces repetitive input, slows iterative exploration, and undermines reproducibility because parameter choices are difficult to record, share, and reuse. We present EZInput, a cross-runtime environment Python library enabling algorithm developers to automatically generate graphical user interfaces that make their computational tools accessible to end-users without programming expertise. EZInput employs a declarative specification system where developers define input requirements and validation constraints once; the library then handles environment detection, interface rendering, parameter validation, and session persistence across Jupyter notebooks, Google Colab, and terminal environments. This "write once, run anywhere" architecture enables researchers to prototype in notebooks and deploy identical parameter configurations for batch execution on remote systems without code changes or manual transcription. Parameter persistence, inspired by ImageJ/FIJI and adapted to Python workflows, saves and restores user configurations via lightweight YAML files, eliminating redundant input and producing shareable records that enhance reproducibility. EZInput supports diverse input types essential for scientific computing and it also includes built-in validation that ensures data integrity and clear feedback that reduces user friction.

Iván Hidalgo-Cenalmor, Marcela Xiomara Rivera Pineda, Bruno M. Saraiva et al.

Life sciences research depends heavily on open-source academic software, yet many tools remain underused due to practical barriers. These include installation requirements that hinder adoption and limited developer resources for software distribution and long-term maintenance. Jupyter notebooks are popular because they combine code, documentation, and results into a single executable document, enabling quick method development. However, notebooks are often fragile due to reproducibility issues in coding environments, and sharing them, especially for local execution, does not ensure others can run them successfully. LabConstrictor closes this deployment gap by bringing CI/CD-style automation to academic developers without needing DevOps expertise. Its GitHub-based pipeline checks environments and packages notebooks into one-click installable desktop applications. After installation, users access a unified start page with documentation, links to the packaged notebooks, and version checks. Code cells can be hidden by default, and run-cell controls combined with widgets provide an app-like experience. By simplifying the distribution, installation, and sharing of open-source software, LabConstrictor allows faster access to new computational methods and promotes routine reuse across labs.

Roberto Santana, Ivan Hidalgo-Cenalmor, Unai Garciarena et al.

In some machine learning applications the availability of labeled instances for supervised classification is limited while unlabeled instances are abundant. Semi-supervised learning algorithms deal with these scenarios and attempt to exploit the information contained in the unlabeled examples. In this paper, we address the question of how to evolve neural networks for semi-supervised problems. We introduce neuroevolutionary approaches that exploit unlabeled instances by using neuron coverage metrics computed on the neural network architecture encoded by each candidate solution. Neuron coverage metrics resemble code coverage metrics used to test software, but are oriented to quantify how the different neural network components are covered by test instances. In our neuroevolutionary approach, we define fitness functions that combine classification accuracy computed on labeled examples and neuron coverage metrics evaluated using unlabeled examples. We assess the impact of these functions on semi-supervised problems with a varying amount of labeled instances. Our results show that the use of neuron coverage metrics helps neuroevolution to become less sensitive to the scarcity of labeled data, and can lead in some cases to a more robust generalization of the learned classifiers.