Metadata integrity in bioinformatics: Bridging the gap between data and knowledge

Open Science at the generative AI turn: An exploratory analysis of challenges and opportunities

Technology influences Open Science (OS) practices, because conducting science in transparent, accessible, and participatory ways requires tools and platforms for collaboration and sharing results. Due to this relationship, the characteristics of the employed technologies directly impact OS objectives. Generative Artificial Intelligence (GenAI) is increasingly used by researchers for tasks such as text refining, code generation/editing, reviewing literature, and data curation/analysis. Nevertheless, concerns about openness, transparency, and bias suggest that GenAI may benefit from greater engagement with OS. GenAI promises substantial efficiency gains but is currently fraught with limitations that could negatively impact core OS values, such as fairness, transparency, and integrity, and may harm various social actors. In this paper, we explore the possible positive and negative impacts of GenAI on OS. We use the taxonomy within the UNESCO Recommendation on Open Science to systematically explore the intersection of GenAI and OS. We conclude that using GenAI could advance key OS objectives by broadening meaningful access to knowledge, enabling efficient use of infrastructure, improving engagement of societal actors, and enhancing dialogue among knowledge systems. However, due to GenAI's limitations, it could also compromise the integrity, equity, reproducibility, and reliability of research. Hence, sufficient checks, validation, and critical assessments are essential when incorporating GenAI into research workflows.

An orchestra of machine learning methods reveals landmarks in single-cell data exemplified with aging fibroblasts

In this work, a Python framework for characteristic feature extraction is developed and applied to gene expression data of human fibroblasts. Unlabeled feature selection objectively determines groups and minimal gene sets separating groups. ML explainability methods transform the features correlating with phenotypic differences into causal reasoning, supported by further pipeline and visualization tools, allowing user knowledge to boost causal reasoning. The purpose of the framework is to identify characteristic features that are causally related to phenotypic differences of single cells. The pipeline consists of several data science methods enriched with purposeful visualization of the intermediate results in order to check them systematically and infuse the domain knowledge about the investigated process. A specific focus is to extract a small but meaningful set of genes to facilitate causal reasoning for the phenotypic differences. One application could be drug target identification. For this purpose, the framework follows different steps: feature reduction (PFA), low dimensional embedding (UMAP), clustering ((H)DBSCAN), feature correlation (chi-square, mutual information), ML validation and explainability (SHAP, tree explainer). The pipeline is validated by identifying and correctly separating signature genes associated with aging in fibroblasts from single-cell gene expression measurements: PLK3, polo-like protein kinase 3; CCDC88A, Coiled-Coil Domain Containing 88A; STAT3, signal transducer and activator of transcription-3; ZNF7, Zinc Finger Protein 7; SLC24A2, solute carrier family 24 member 2 and lncRNA RP11-372K14.2. The code for the preprocessing step can be found in the GitHub repository https://github.com/AC-PHD/NoLabelPFA, along with the characteristic feature extraction https://github.com/LauritzR/characteristic-feature-extraction.