Postdoc in Large Language Models and Agentic AI for Pathogen Analysis - DTU Food

DTU - Technical University of Denmark; Kongens Lyngby; Sur place; DKK 520 000 - 700 000; Plein temps

Résumé du poste

DTU National Food Institute seeks a postdoctoral researcher to advance AI-driven pathogen analysis for GPAP. You will lead multimodal LLMs and agents, train on diverse datasets, and collaborate with international partners to build scalable knowledge systems for public health data.

The role combines methodological research with software development, publishing in top venues, and contributing to an international research infrastructure used by scientists and public health professionals worldwide.

Qualifications

• Strong research background in computer science, machine learning or a closely related field.
• Excellent written and spoken English with ability to explain complex concepts clearly.

Responsabilités

• Develop multimodal LLMs and agents capable of writing and executing code to extract and organize metadata.
• Collect examples from GPAP partners and through AI-assisted research, curate training data, and build benchmarks for metadata identification.
• Investigate LLM post-training, including agentic reinforcement learning and on-policy distillation methods, for metadata processing and scientific analysis.
• Build agent environments that connect models with bioinformatics pipelines, databases and scientific software, and integrate them into GPAP’s agentic AI service.
• Evaluate agents for pathogen analysis, interpretation and scientific reporting, with attention to reproducibility and traceability.
• Lead research and software development projects involving MSc and PhD students and other postdoctoral researchers, coordinating planning, implementation, code reviews and delivery within an agile team.
• Publish research in leading AI conferences and scientific journals and communicate to GPAP collaborators and partners across disciplines.

Connaissances

Python programming

Machine learning

Research

English proficiency

Post-training LLMs

Agent development

Code reviews

Formation

PhD degree

Outils

Python

CI/CD

LLM serving/infrastructure

Bioinformatics pipelines

Description du poste

Job DescriptionJoin an international effort to build an AI-powered infrastructure for global pathogen surveillance. The Global Pathogen Analysis Platform (GPAP), supported by up to DKK 200 million from the Novo Nordisk Foundation, brings together DTU, the University of Copenhagen, Statens Serum Institut and Imperial College London, alongside collaborators across Europe, Africa, Asia and the Americas. GPAP is developing a freely accessible platform combining advanced bioinformatics, AI agents and secure data collaboration to support infectious disease surveillance across human, animal and environmental health. Its mission is to give researchers and public health teams in low, middle and high-income countries the tools to analyze their data locally and act on the results.

Job DescriptionJoin an international effort to build an AI-powered infrastructure for global pathogen surveillance. The Global Pathogen Analysis Platform (GPAP), supported by up to DKK 200 million from the Novo Nordisk Foundation, brings together DTU, the University of Copenhagen, Statens Serum Institut and Imperial College London, alongside collaborators across Europe, Africa, Asia and the Americas. GPAP is developing a freely accessible platform combining advanced bioinformatics, AI agents and secure data collaboration to support infectious disease surveillance across human, animal and environmental health. Its mission is to give researchers and public health teams in low, middle and high-income countries the tools to analyze their data locally and act on the results.

We are looking for a postdoctoral researcher in large language models and agentic AI to join GPAP’s AI Research Team at DTU National Food Institute. You will develop multimodal models, investigate LLM post-training and build agents that connect scientific metadata with pathogen analysis workflows. The role combines methodological research with software development: you will lead projects, publish in leading scientific and AI venues and integrate your methods into an international research infrastructure being developed with the scientists and public health professionals who will use it.

Responsibilities And Qualifications

You will join as a senior technical member of the AI Research Team within GPAP. A central project will reduce the manual preparation needed before users can analyze their data, by automatically organizing metadata and matching it to the relevant samples and datasets. This metadata often arrives in inconsistent formats, scattered across spreadsheets, PDFs, images, webpages, notes and scripts. You will develop multimodal LLMs and coding agents that automatically extract and standardize this information, then match it to the corresponding samples and datasets uploaded by users or already available on GPAP. Alongside this project, you will also contribute to LLM post-training and agent development for pathogen analysis, working closely with Dr Harrison Bo Hua Zhu, Professor Samir Bhatt (University of Copenhagen and Imperial College London), Professor Frank Møller Aarestrup, and GPAP researchers and engineers.
Your main tasks will be to:

• Develop multimodal LLMs and agents capable of writing and executing code to extract and organize metadata.
• Collect examples from GPAP partners and through AI-assisted research, curate training data, and build benchmarks for metadata identification.
• Investigate LLM post-training, including agentic reinforcement learning and on-policy distillation methods, for metadata processing and scientific analysis.
• Build agent environments that connect models with bioinformatics pipelines, databases and scientific software, and integrate them into GPAP’s agentic AI service.
• Evaluate agents for pathogen analysis, interpretation and scientific reporting, with attention to reproducibility and traceability.
• Lead research and software development projects involving MSc and PhD students and other postdoctoral researchers, coordinating planning, implementation, code reviews and delivery within an agile team.
• Publish research in leading AI conferences and scientific journals and communicate to GPAP collaborators and partners across disciplines.

We are looking for

• A strong research background in computer science, machine learning or a closely related field.
• An interest in AI for Science but bioinformatics background is not required.
• Experience in LLM post-training and benchmarking/evaluation.
• Experience building agent harnesses and the software environments used to run and evaluate them.
• Strong Python programming and software engineering skills, including testing, version control and collaborative development.
• Experience with CI/CD, LLM serving/infrastructure and/or distributed systems.
• Excellent written and spoken English. The ability to explain complex technical concepts clearly in presentations and discussions with collaborators and partners across disciplines, including those without an AI background.
• Relevant publications, research software and open-source contributions will be considered in the assessment.

As a formal qualification, you must hold a PhD degree (or equivalent).

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply. As DTU works with research in critical technology, which is subject to special rules for security and export control, open-source background checks may be conducted on qualified candidates for the position.

DTU National Food Institute

DTU National Food Institute conducts research into and disseminates - through advice, innovation and teaching - sustainable and value-creating solutions in the area of food and health for the benefit of society. The vision is to make a difference by generating future prosperity through research into food and health. The institute works to prevent disease and promote health, develop new and better food products for a growing population and create sustainable technological solutions, including biosolutions. The institute’s tasks are carried out in interdisciplinary collaboration within e.g. nutrition, chemistry, toxicology, microbiology, epidemiology, modelling, and technology. This is achieved through a strong academic environment of international top class with correspondingly skilled researchers and employees. The Institute employs approximately 390 staff members.

The DTU National Food Institute conducts research, education and scientific advisory work in food and health. GPAP brings together researchers in AI, bioinformatics, pathogen genomics and public health to make advanced analysis tools accessible to scientists and public health authorities worldwide. You will work within a collaboration involving DTU, the University of Copenhagen, Statens Serum Institut, Imperial College London and international partners.

DTU – For the benefit of society since 1829

DTU is one of Europe's leading elite technical universities. Through research and education at an international top level, we create solutions to the major societal challenges of our time and help secure Europe’s global leadership in sustainable technological development. Since Hans Christian Ørsted founded DTU almost 200 years ago, our mission has remained the same: We develop and create value through the natural and technical sciences for the benefit of society. DTU has 13,800 students, 1,600 PhD students, and 6,500 employees. We work in an international environment and have an inclusive, stimulating, and informal work culture. DTU has campuses in all parts of Denmark and in Greenland and collaborates with the best universities around the world.

We offerDTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and terms of employmentThe appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. In addition, supplements can be negotiated in accordance with DTU’s salary structure for scientific staff: www.inside.dtu.dk/en/human-resources/during-employment/salary/salary-structures .
The period of employment is 3 years. The position is full-time, with a starting date of 1 December 2026 (or according to mutual agreement).
You can read more about career paths at DTU here .

Further informationFor further information about the research project and position, please contact Dr Harrison Bo Hua Zhu at [e-mail] at DTU National Food Institute.
Read more at https://www.food.dtu.dk/english/research/genomic-epidemiology and for GPAP please visit https://gpap.global/ .
If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark .