PhD position in Large Language Models for Multimodal Spatial Omics in Melanoma — SPACE-MEL DC9

Reference Number: SPACE-MEL — DC9 — GA 101311007

Is the Job related to staff position within a Research Infrastructure?: No

Offer Description

Supervisor: Dr. Jon Pey, Intelligent Biodata SL, Spain.

Academic co-supervisor: Prof. Ángel Rubio, University of Navarra, TECNUN School of Engineering, San Sebastián, Spain.

Additional co-supervisors and secondment hosts: Prof. Alejandro Sifrim, KU Leuven, Department of Human Genetics, Belgium (Academia); Dr. Samantha Perona, Spotlight Pathology Ltd., United Kingdom (Industry).

Project description

DC9 will develop and implement a Large Language Model (LLM)-based system for natural-language exploration of multimodal spatial embeddings in melanoma research. The project will use spatial multi-omics, histology-derived features and consortium-generated datasets to support intuitive querying and interpretation of complex melanoma data.

The project pursues two integrated objectives: (i) fine-tune pretrained LLMs for melanoma-relevant spatial multi-omics data; and (ii) develop an accessible interface that enables clinical and research users to explore integrated datasets without advanced computational expertise.

At Intelligent Biodata, the candidate will benchmark and adapt existing LLM architectures for spatial multi-omics applications, using public datasets and SPACE-MEL data to improve model accuracy and relevance. During a first secondment with Prof. Alejandro Sifrim at KU Leuven, the candidate will receive training in multimodal data fusion and representation learning. A second secondment at Spotlight Pathology Ltd., supervised by Dr. Samantha Perona, will focus on developing a user-friendly graphical interface for clinical and research users.

Expected outcomes include: (1) an LLM for spatial multi-omics; (2) integrated melanoma datasets; and (3) an accessible software tool for non-computational users.

Host institution and doctoral training

The doctoral candidate will be employed by Intelligent Biodata SL in Spain under the industrial supervision of Dr. Jon Pey. The academic component of the doctoral training will be conducted in collaboration with the University of Navarra, particularly the TECNUN School of Engineering in San Sebastián, under the academic co-supervision of Prof. Ángel Rubio.

The candidate will benefit from complementary industrial and academic environments, with activities at both Intelligent Biodata and the university.

Intelligent Biodata is a bioinformatics company with expertise in artificial intelligence, machine learning, natural language processing, multimodal data integration, bioinformatics pipelines and software development for biomedical applications. The company develops computational methods and deployable software solutions for the analysis of complex multi-omics, imaging and clinical datasets.

The host offers access to development and production infrastructure for AI model implementation, testing, deployment and monitoring, including GPU resources, cloud computing and secure data-transfer infrastructure with KU Leuven. The candidate will benefit from expertise in model development, biomedical data integration, software engineering and deployment of AI solutions for precision medicine.

Secondments

The project includes research and training visits to the following partner organisations. A willingness to travel and spend time abroad is essential:

• Six months at KU Leuven, Department of Human Genetics, Belgium, supervised by Prof. Alejandro Sifrim.
• Three months at Spotlight Pathology Ltd., United Kingdom, supervised by Dr. Samantha Perona.

The SPACE-MEL consortium

SPACE-MEL is an EU-funded MSCA Doctoral Network advancing spatial single-cell omics technologies for precision medicine. The consortium brings together European universities, technology providers, clinical partners and companies to address experimental and computational challenges limiting the clinical translation of spatial biology.

By integrating multi-omics approaches, enabling the transition from 2D to 3D tissue analysis and developing advanced data interpretation methods, SPACE-MEL aims to improve our understanding of cellular organisation and disease mechanisms.

The network will train 15 doctoral candidates through an interdisciplinary programme spanning spatial imaging technologies, molecular biology, computational biology, pathology and biomarker discovery. Cross-sectoral secondments, hands-on research and transferable-skills training will provide experience across the spatial biology workflow.

What SPACE-MEL offers

• A three-year MSCA-funded doctoral research position.
• Doctoral training combining industrial and academic supervision.
• Participation in international courses, workshops and conferences.
• Research visits to academic and industrial partners.
• An international, interdisciplinary research environment.
• Remuneration in accordance with the applicable MSCA Doctoral Networks funding conditions, including mobility support and a family allowance where applicable.

This position is funded by the European Union under the Horizon Europe Marie Skłodowska-Curie Actions programme, SPACE-MEL, Grant Agreement No. 101311007.

Where to apply

E-mail: jon@intelligentbiodata.com

Requirements

Research Field: Computer science » Other

Education Level: Master Degree or equivalent

Skills/Qualifications

• Master's degree (or equivalent) in Computer Science, Artificial Intelligence, Bioinformatics, Computational Biology, Biomedical Engineering, Data Science, Mathematics, Physics, or a closely related field.
• Solid programming skills in Python.
• Good understanding of machine learning, preferably including deep learning and/or natural language processing.
• Strong interest in large language models, multimodal AI or foundation models, and their application to biomedical research.
• Experience with software development, version control (e.g. Git) and collaborative coding practices.
• Experience with scientific computing libraries such as PyTorch, TensorFlow, scikit-learn, NumPy or Pandas is desirable.
• Previous exposure to bioinformatics, computational biology, spatial omics or biomedical data analysis is advantageous but not mandatory.

Specific Requirements

• Motivation to work in an interdisciplinary environment combining artificial intelligence, biomedical research and software development.
• Ability to work independently while contributing effectively to an international multidisciplinary team.
• Strong analytical, problem-solving and organisational skills.
• Good communication skills, both oral and written.
• Proficiency in English is required. Successful candidates will need to demonstrate their English proficiency through a recognised test (e.g. IELTS, TOEFL or Cambridge English), an applicable exemption, or confirmation by the supervisor, subject to the doctoral programme's admission requirements. Exemptions may apply to candidates from majority English-speaking countries or those whose degree was taught and assessed in English.
• Knowledge of Spanish is advantageous for day-to-day interactions but is not required.
• Willingness to travel and undertake the planned international secondments: six months at KU Leuven, Belgium, and three months at Spotlight Pathology Ltd., United Kingdom.

Languages: ENGLISH

Level: Excellent

Additional Information

Benefits

• A full-time doctoral research position with 36 months of funding through the SPACE-MEL Marie Skłodowska-Curie Doctoral Network.
• Employment with Intelligent Biodata SL in Spain, with doctoral training in collaboration with the University of Navarra, TECNUN School of Engineering.
• An estimated gross annual salary of approximately EUR 41,000, including the mobility allowance. The exact gross salary will be determined before the employment contract is signed, based on the applicable employer social security contributions. The stated gross salary excludes employer social security contributions and is subject to employee social security contributions and applicable income tax.
• An additional family allowance where applicable, in accordance with the MSCA rules and the candidate's eligibility.
• Joint industrial and academic supervision, combining AI research, biomedical applications and software development.
• Access to GPU resources and infrastructure for AI model development, testing and deployment.
• International secondments at KU Leuven, Belgium (six months), and Spotlight Pathology Ltd., United Kingdom (three months).
• Participation in network-wide scientific training, transferable-skills activities, workshops and conferences.

Eligibility criteria

Applicants must fulfil the following conditions:

• Doctoral status: applicants must not hold a doctoral degree at the date of recruitment. Researchers who have successfully defended their doctoral thesis but have not yet formally received the degree are not eligible.
• Mobility rule: applicants must not have resided or carried out their main activity, such as work or studies, in Spain for more than 12 months during the 36 months immediately preceding their recruitment date, subject to the exceptions provided by the applicable MSCA rules.
• Academic eligibility: applicants must hold a relevant Master's degree or equivalent qualification and fulfil the admission requirements of the doctoral programme at the University of Navarra.
• Applicants may be of any nationality.
• The selected candidate must enrol in the agreed doctoral programme and participate in the research and training activities of the SPACE-MEL network, including the planned international secondments.

Eligibility will be checked against the applicable MSCA Doctoral Networks rules and the doctoral programme's admission requirements.

Selection process

Applications must be submitted in English by email to jon@intelligentbiodata.com, with the subject line "SPACE-MEL DC9 application – [Applicant's full name]".

Required documents:

• A statement of interest, limited to 2,500 characters, explaining the applicant's motivation for the fellowship and the relevant qualities and experience they would bring to the project.
• A curriculum vitae including education and relevant research or professional experience.
• Academic transcripts showing university examinations and marks.
• A final degree certificate translated into English. Applicants whose final certificate is not yet available should indicate their expected completion date. The required qualification and supporting documentation must be available in time to meet the recruitment and doctoral admission requirements. Translation and legalisation requirements will follow the University of Navarra's admission procedures.

Selection will comprise an eligibility check, an assessment of the application documents and interviews with shortlisted candidates. Assessment will consider academic background, relevant technical skills and experience, motivation, and suitability for the project and its training programme.

Shortlisted candidates will be asked to provide contact details for up to two referees.

The selection committee will include representatives of the recruiting organisation, academic supervision and an industrial secondment partner, in accordance with the SPACE-MEL recruitment procedure.

Recruitment will be open, transparent, merit-based, impartial and equitable, with equal opportunities for all applicants.

Work Location(s)

Number of offers available: 1

Company/Institute: Intelligent Biodata SL

Country: Spain

State/Province: Gipuzkoa

City: Lasarte

Postal Code: 20160

Contact

City: Lasarte

Website: https://www.intelligentbiodata.com/

Street: Pol. Ind. Errekalde 59 1

Postal Code: 20160

E-Mail: jon@intelligentbiodata.com