Aarón Ayllón Benítez

AI / ML Leader · Product & Platform Strategy · Research ↔ Production

PhD Computer Science · MSc Artificial Intelligence · Four years line-managing ML teams at BASF Digital Solutions. I build the bridge between research rigor and production pragmatism.

Español English Français
Aarón Ayllón Benítez

Executive Summary

Leading ML teams is a translation problem — between research and production, between long-term R&D and short-term commitments, between what models can do and what the business actually needs. I have spent the last four years doing that translation at BASF Digital Solutions, scaling direct reports from 8 to 16 within a 60-person multi-function portfolio, and leading two production ML platforms adopted across multiple internal teams.

My path is deliberate: PhD in Computer Science (Bordeaux), MSc in Artificial Intelligence, postdoctoral research applying ML to gene regulatory networks, first-author publications in Q1 journals and IEEE, and competitive research grants as main author — followed by industry because the most interesting ML problems are the ones that have to ship. Portfolio decisions, team scaling, and platform thinking are where I operate best.

Focus Areas

  • Production ML platforms & self-service data products
  • Portfolio rationalization, ROI-driven decisions, cost avoidance
  • People leadership: hiring, performance, career paths, underperformance management
  • Computer vision, time-series forecasting, knowledge graphs, GenAI applications
  • Research-to-production translation & AI-native engineering culture
  • Cross-functional alignment: business, engineering, data science, operations

Selected Projects & Platforms

Four initiatives that illustrate how I bridge research and production — from academic tools adopted by bioinformatics communities to enterprise ML platforms with measurable business impact.

⚙️
Production Platform
Computer Vision Platform

Led a Computer Vision platform offering reusable templates for classification, segmentation and detection — now in production across multiple internal teams. Delivered multi-million-euro cumulative cost savings during my ownership.

📈
Self-Service Platform
Forecasting Platform

Led evolution and maintenance of a self-service time-series forecasting platform aimed at business users rather than data scientists — generating significant recurring annual savings for the organisation.

🧬
Research Software
GSAn

Interactive web platform transforming high-throughput gene data into actionable biological insights. Published in NAR Genomics and Bioinformatics (Q1, 2020). Used by researchers as an alternative to classical enrichment analysis.

🌱
Research + Industry
EPPO Ontology

Contributed to an internal ontology integrating regulatory and biological data. Enabled flexible data extraction, improved decision-making and reduced manual effort in crop-protection workflows. Published in Frontiers in AI (2023).

Experience

Publications

First-author peer-reviewed publications in Q1 journals and IEEE proceedings. Click on any item to expand details.

EPPO Ontology: A Semantic-Driven Approach for Plant and Pest Codes Representation

Frontiers in Artificial Intelligence · 2023 · Industry
+
A. Ayllon Benitez, J.A. Bernabe Diaz, I. Esnaola Gonzalez, P.P. Espinoza Arias, B.C. McCaig, K. Hanzlik, D.S. Beeckman, T. Cools, C. Castro Iragorri, N. Palacios

Presents the development of an internal BASF ontology representing EPPO plant and pest codes, enriched with NCBI Taxon data. Describes the adoption of the ontology within BASF's Agricultural Solutions division and the lessons learned.

Ontology Management in an Industrial Environment: The BASF Governance Operational Model for Ontologies (GOMO)

ISMB 2022 — Bio-Ontologies Community · Madison, WI · Industry
+
A. Iglesias-Molina, J.A. Bernabé-Díaz, P. Deshmukh, P. Espinoza-Arias, A. Ayllón-Benítez, A. Fernández-Izquierdo, J.M. Ponce-Bernabé, S. Pérez, E. Ruckhaus, O. Corcho, J.L. Sánchez-Fernández

Presents BASF's Governance Operational Model for Ontologies (GOMO), a framework addressing all stages of the ontology lifecycle within a large industrial organisation. Collaboration between BASF Digital Solutions and the Ontology Engineering Group (UPM).

Federating and querying heterogeneous and distributed Web APIs and triple stores

ISMB 2022 — Bio-Ontologies Community · Industry
+
T. Mendes de Farias, C. Dessimoz, A. Ayllón-Benítez, C. Yang, J. Long, A.-C. Sima

Proposes a federated data integration architecture within an industrial setup, using an ontology-based data access method to homogenise fragmented Web APIs and triple stores at BASF. Most queries answered in under 1 second.

Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data

Nature Communications · 2021 · Q1 · IF 17+
+
M.C. Altman, D. Rinchai, N. Baldwin, M. Toufiq, E. Whalen, M. Garand, B. Syed Ahamed Kabeer, M. Alfaki, S.R. Presnell, P. Khaenam, A. Ayllón-Benítez, F. Mougin, P. Thébault, R. Thiebaut, et al.

Large multi-author collaboration in Nature Communications presenting BloodGen3, a reusable framework of 382 transcriptional modules for analysing blood transcriptome data across immunological states. My contribution: functional annotation of modules using GSAn.

GSAn: a Web server as an alternative to enrichment analysis for annotating gene sets

NAR Genomics and Bioinformatics · 2020 · Q1 · First author
+
A. Ayllon-Benitez, R. Bourqui, P. Thébault, F. Mougin

Presents GSAn, a web server offering an alternative to classical over-representation analysis. Clusters semantic relationships between annotation terms to provide richer, more interpretable gene-set annotations.

A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets

PLoS ONE · 2018 · First author
+
A. Ayllon-Benitez, F. Mougin, J. Allali, R. Thiébaut, P. Thébault

Introduces a novel evaluation methodology for semantic similarity measures applied to gene set annotation, quantifying how measure choice affects downstream biological interpretation.

Deciphering gene sets annotations with ontology-based visualization

IEEE 21st International Conference on Information Visualization (IV) · London · 2017 · First author · Invited talk
+
A. Ayllon-Benitez, P. Thébault, J.T. Fernández-Breis, M. Quesada-Martinez, F. Mougin, R. Bourqui

Proposes an ontology-driven visualization approach for interpreting gene set annotations. Invited talk — travel grant awarded by the Société Française de BioInformatique (SFBI).

Teaching & Mentoring

100+ hours of university teaching at the masters and bachelor's level, plus mentoring of 25+ students across four academic years — covering bioinformatics, databases and computer science fundamentals.

University Teaching
Course Institution & Level Year Hours
Applied Functional Genomics (VT20) Umeå University · Master in Biology (2nd semester) 2019–2020 40
Introduction to Databases (M1104) Université de Bordeaux · DUT Informatique 2017–2018 54
Introduction to Environment Systems (M1101) Université de Bordeaux · DUT Informatique 2017–2018 10
Total 104
Student Mentoring
Year Level Students Duration
2019 2nd year Master in Software Engineering 7 2 months
2018 2nd year Bachelor in Biology 1 2 months
2018 2nd year Master in Software Engineering 8 2 months
2017 1st year Master in Bioinformatics 4 2 months
2016 1st year CS Engineering 1 2 months
2016 1st year Master in Bioinformatics 4 2 months

Editorial & Peer Review

Guest Editor

Plants (MDPI, Q1) — Special issue: "Bridging the Annotation Gap in Non-Model Plant Species". 2020–present. JCR category rank 58/234 (Q1) in Plant Sciences. Keywords: gene annotation, non-model organisms, gene network inference, machine learning.

Journal Peer Review
  • Microorganisms (MDPI) — Reviewer · 2020
Conference Peer Review
Conference Role Location Year
useR! 2020 — The R User Conference Sub-reviewer Virtual 2020
16th ISCB Student Council Symposium Sub-reviewer Virtual 2020
15th ISCB Student Council Symposium Sub-reviewer Switzerland 2019
3rd BR-SCS Network(ING): ISCB Brazilian Student Council Symposium Sub-reviewer Brazil 2018
4th International Conference on Technologies and Innovation (CITI) Reviewer Ecuador 2018

Talks & Public Speaking

Industry Talks & Podcasts
  • Cluster IA Comunidad de Madrid · Podcast: "Build vs Buy vs Open Source in GenAI" · Apr 2026
  • Expoquimia 2023 · Barcelona · Industry talk: "Supporting the chemical industry through advanced image analysis"
  • TECNALIA · Podcast: "Tecnología, Pasión y Futuro" · Jun 2023
Scientific Communication
  • My PhD in 1024 characters · Published essay · Bulletin de la société informatique de France · Nov 2019
  • SMS Debate (Science-Media-Society) · TousEnScience · Bordeaux · 2018 & 2019 editions
  • Scientific Game Jam Bordeaux · 1st Prize — video game based on PhD research · Mar 2018
  • My PhD in 180 seconds (MT180s) · French PhD pitch competition · Bordeaux · Feb 2018

Education

MSc Artificial Intelligence

Universidad Internacional de La Rioja (UNIR) · 2023–2024

UNIR
PhD in Computer Science (Informatics)

Université de Bordeaux / LaBRI · Ministerial funding (MESR) · 2016–2019

UB
MSc Bioinformatics (Avg. 9/10)

University of Murcia · 2014–2015

UMU
BSc Biochemistry

University of Murcia · 2009–2013

UMU